Disable Device is an infiltration and sabotage based skill -- disabling traps and locks are its most common uses by far, but it's also an ability that allows you how to figure out how to fastest disable other machines as well (sabotage the mill so it can't grind flour and disrupt the food supply, etc.).
Eliminating it and requiring different craft skills for different forms of machine/structure disruption would be possible--you know how to break it if you know how to make it, after all. (Although it eliminates the idea that you might have an understanding of how to throw a wrench in the works appropriately but not put it back together.)
Where it would make things harder for trapfinding characters (including rogues with the trapfinding feature, investigators, archeologist bards, urban rangers, etc.) is it would create a "skill point tax" -- they would have to spend more skill points to be able to do what they could do before as far as their infiltration skills go. Pathfinder made the effort to combine Pick Locks and Disable Device into one skill, and this "consolidation" would instead in some respects actually undo that streamlining effort. Especially if you did, just in case, want the option of disabling other systems.
The upside of course is that of course these characters would become MORE skilled in terms of being able to CREATE various useful things without having to separately purchase the skill. Rogues with a high Intelligence would potentially benefit from this most as they have the most skill points to freely spend as they wish. (A bard's versatile performance technically represents "more" skill points, but at higher levels only, and is limited to providing "free points" to only a total of 8 different skills---and moreover, one of the bards with anything akin to the trapfinding ability--for maximal usage of it--is the archeologist, who does not get the versatile performance ability.) At the same time, a rogue with a bucket of Craft/Profession skills may, depending on your perception of the class, stop "feeling" like a rogue (the same goes for an archeologist, urban ranger, etc.).
You could consider perhaps Knowledge (Engineering) another consolidation option, even though Knowledge skills more represent knowing than doing.... but you'd have to be sure relevant classes or archetypes gained that as a class skill. There you probably would be freeing up MORE skill points, and it depends on how you feel about that as to whether it would feel worth it to you.
As a general rule, I do allow cross-use of skills if the player can make a case for it and I think your two suggestions are certainly reasonable. Profession skills are, by the book, pretty useless so I like rewarding creative applications of them.
I don't see anything wrong with this. It doesn't replace the trapfinding class feature. Putting a rank into Craft (trap) still isn't as valuable as putting a rank in Disable Device for disabling stuff. In addition, there's a precedent for some skills being used for others.
Generally speaking, using a specific skill as a substitute for a general skill (as in your example) should be fine. Keep in mind though that this will allow some characters to pick specific skills with more favorable key abilities than those applied to the general skills. (You could rule that a character using Craft (traps) as a substitute for Disable Device has to apply their Dex modifier in place of their Int modifier to their skill check.)
Using a general skill as a substitute for a specific skill could work as well, provided it makes sense, but it should incur a penalty.
I was not thinking of eliminating Disable Device, but allowing Craft(traps) to disable traps, Profession(locksmith) to pick locks, etc. in addition to Disable Device.
I don't see a problem with that. While more classes have Craft and Profession as class skills, it wouldn't take away from trapfinding classes/roles. If worried about balance (a Wizard with buckets of skill points who could disable and pick might seem to be able to do too much) you could boost the DC if using the relevant Craft or Profession skill rather than Disable Device -- which also ensures that Disable Device doesn't feel redundant.
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You may want to allow a player to use it, but only for mechanical traps and snares, but the character could not use Craft (traps) to pick locks, since he does not have knowledge of building locks.
Another idea would be to add a +2 Insight bonus to Disable Device for every 5 ranks of Craft (traps), again for disabling traps only.
I once tried to map out synergistic skills like that but it got too crazy and gave up.