Unless this has been errata'ed, the answer is 'yes', and it doesn't affect the casting time.
Remember, though, that it's a once-a-day thing, and that there are a number of ways to _really_ ruin that caster's day:
1) Ring of Counterspells. Most people won't have them, but conversely some will. And, if the Wizard is using a common spell, he's stuck. Remember that a normal Fireball can be used to counterspell a Maximised Empowered Fireball.
2) Normal counterspelling. If this tactic is being overused, have your NPC casters adapt by using counterspells more often. (They may even hire an apprentice who's sole job is to use an array of scrolls for that purpose... although I'm less than 100% sure you can counterspell with a scroll.)
3) Spell Immunity. Again, if he's using a common spell, this defense will work wonders.
4) Good old evasion/high saving throws.
5) If it really bugs you, hit them with exactly the same tactic a few dozen times. Then, offer to drop the tactic provided they accept a 'no more than one sudden metamagic feat per spell' restriction. After all, whatever they can do, you can _always_ do better.
Also be sure to enforce the 1/day nature of the tactic, and be sure to make it appropriately hard for the group to do the whole fight/rest thing, where they use all their resources in the first combat of the day and then immediately retreat to rest.
(To be honest, I think the Sudden Metamagic feats are just a little bit too good, especially Empower and Maximise. At the very least, I think the 'base' feat of the same name should be added to the list of prerequisites. But that's another post for another day, I think.)
I allow it, and most of my casting class players take "Sudden Maximize" feat early on. There might be something a little too strong about the feat but not over much so. The other way around the players "over" use of that feat is more than one or two encounters per day. Our game still uses the 3.0 edition rules of bull strength, cats grace etc and the sudden maximize feat is a great choice for the cleric. Between the cure spells and the buffing spells in makes a magic a greater factor in the game.
It sounds like your players need to be challenged more by magic using opponents. This will boost your comfort level with metamagic feats and spells (it most certainly did mine) while giving the game a more fantasy feel. In the past I have used 4 sorcerous (2nd level ) goblins (elite array) with scrolls or mirror image, using the augmen summoning feat, with two wands of summon monster (1st or 2nd level wands with 3 to 7 charges, and two wands of magic missile (caster level 1st or 3rd, 5 to eight charges. It is a super fun encounter, especially with a terrain/line of sight impedment. I have used a chasm with a 15 foot long board across it so Pc's can only get there one at a time, or on a cliff where pcs can only climb up one at a time. I have used bad guy minions wih sudden maximize on thier healing/buffing spells to keep the fight going longer, and make clashes more dramatic. A gnoll druid with sudden empore/maximized call lightning makes a very entertaining wilderness encounter.
Another out is to give your players an encounter or two a session where the sudden spells are not called despite appearances, Figure out a way to have the player taste thier own spells once in a while. A wall of force or glass that blocks the offending players fire ball while he is in the blast area would be particularly devious. also if you can craft situations where thier feat choices come back to haunt them, where they recognize thier weakness in focus on two metamagic feats early on, and not having other more general feats that boost saving throws, accuracy, and skill check results.
Sudden maximized and sudden empowered spells work very well on groups of a many monsters at lower levels. Against fewer foes at higher levels these feats are almost required just to make the encounters balanced and npcs can be modified to accomidate player choices. most certainly your big baddie has an intelligence source that tells him of the players weaknesses as well as strengths. Just as your players are likely to do intelligence gathering and contact cultivation. Good luck, have fun with it!