The GM has to know about your protections, it's just how this game works. Admittedly if you are going to that level to protect the books, nothing short of a CR 7+ is going to be able to just walk up, make your books go *poof* and then wander out again.
Given the wealth you will be starting with, I would recommend both of you pick up 'secondary' Spellbooks and start scribbling down spells and stockpiling Scrolls in a safe place in case of Shenanigans, just to fully insure yourselves.
I would turn to the GM and say, nicely, that you and the other player would like to avoid being gimped for several games because he was clever and burned your spellbooks ..... now stealing them and selling them to other Wizards, that would work as a fully-stocked Spellbook is quite valuable to any Wizard.
Other than using Craft Wondrous Item on a chest to make it shoot Magic Missile if the correct key is not used, and to use a very audible Alarm spell if picked up without the correct command word, is about all you can do .... but with only 9k between you, I would recommend just a solid chest and some superior locks, and maybe a well-trained Guard Dog or three to sit watch at night over them.
I personally feel that a DM who intentionally and repeatidly targets bond items, spell books, and spell component pouches isn't neccessarialy making the best choices for his NPCs nor is he holding fun and enjoyment of the game to be all that important of an aspect. Perhaps once, maybe twice over the course of many levels I'd as a DM would target a casters books/bonds/familiars/components, but would only do it for the most tatical of villians or as part of the story, such as a thief getting caught in the attempt, either intentionally (from the NPCs point of view) or unexpectantly.
NPCs may be kept guessing as to what your bond is, if you are holding or wearing several items of good quality that could qualify to be a bond. It'd be up to your DM to decide how common of knowledge what a wizards bond could be outside of other arcane casters. Obviously if you chose the familar option it owuld be far more overt as to your choice, but you'd also risk less.
When I run a game, if a player wants to use contingent spells, or trap their hide out, or the like, I have them write it down, and I fold it up and set it aside, that way I can't even subconciously give a NPC a defense or way around it if they weren't prepared, but I have a way to check to see what the contengency was and make sure my players aren't "cheating" when it comes up. You might be able to get you DM to do the same...maybe.
Ignoring that it is usually a better choice to damage a caster than spend an NPC's round trying to remove some of their basic gear, wealth, and abilities simple things such as fire traps, glyphs (the blasting options may hurt the item but a spell glyph with a suggestion to return the property so the mage doesn't seek horrible vengence with unfettered arcane power is a decent choice), and other magical traps can be useful. If your bond is a ring I recomend the explorer's outfit for clothing (it comes with gloves; lets see your ring get stolen or damaged when an NPC can't even see it to know that it is there). Perhaps carry several large tomes (maybe some filled with erotica or obscure and inaccurate history, or old warehouse ledgers) with you if you are really paranoid, thus giving a decent chance that a sneak who tries to run off with or a fighter who tries to break your book gets something useless instead. Or just keep it in a pack and see if your DM will let you arcane lock it.
When you reach higher levels keep only a small traveling book of regular spells on you and keep your master list in an extradimensional space, such as a secret chest or in your well fortified home base and teleport back to it as needed, coupled with alarm spells. The bond is of masterwork quality and though it is up for debate as to whether or not your DM would consider it innately magical you may be able to mark it with an instant summons.
At any rate, if your DM does try to knick your spells from you (there are a few useful feats to avoid this - mastery, eschew materials) I hope he compensates for it in the CR and treasure departments.
Given the wealth you will be starting with, I would recommend both of you pick up 'secondary' Spellbooks and start scribbling down spells and stockpiling Scrolls in a safe place in case of Shenanigans, just to fully insure yourselves.
This is really the only option you have. The Advanced Players' Guide has a Traveling Spellbook on p. 182 & 187 that is 50 pages instead of the "heavy" 100-page normal spellbook for 10 gp instead of 15 gp. Start copying your main spellbook into traveling spellbooks and leave them at strongholds, well-known NPC houses, etc.
Spell Mastery and Eschew Materials can help you memorize your most crucial spells, but now you've lost your entire feat tree and leveling ladder to what you wanted your Wizard to be. Start crafting scrolls, Wands and various Wondrous Items to reduce the need to rely upon your spellbook. (Shrinking Glove of Storing can hide your spellbook from thieves, and you keep it on your hand at all times. Ignore the Michael Jackson jokes.) If you have a team member to help you out with crafting you might be saved. Your goal is a Blessed Book securely stored upon your person.
I would be more afraid of your GM targeting your familiar or bonded item - you lose the bonded item, and you are helpless for about a week until you can make/bond with a new item. That's far more damaging. You can pick up a spellbook from anywhere and with a high Spellcraft roll be back in business in a day or two.
You need to have a private person-to-person talk with this GM. If they are intentionally screwing the magic-users in the campaign because, deep down, they really don't like magic in their campaign and they are trying to minimize it to make a low-magic campaign, then you either accept this or leave the GM's table. A GM who resorts to trickery to keep "the players on their toes" is actually lacking in imagination, and also not playing to the spirit of the game. I'd like for this GM to have a table full of high arcane rules lawyers facing him or her.
IIRC there is the Geas spell too that has something to help stop people from just picking stuff up.
I'm very fond of spell mastery, still spell, silent spell, and eschew materials myself, and have yet to regret taking them.
There is the harden spell which will make your book harder to distroy (it's in the campaign settings guide), and iirc there is a second level spell that helps protect books (look for it on the PFsrd website).
Also consider commissioning a special spell book built of alternate materials -- the 3.5 D&D book "complete arcane" had a nice little section in the back about doing just this and I recommend the book for that, and the good RP material it has in back about playing arcanist in general -- even if you never use any of the crunch in the book.