Are Missiles the Ultimate Meta...
No. They are the Dark Side of the the Force. Easier, faster, more seductive, but not stronger.
...Or can missile defenses eventually negate them?
Yes. Anything your opponent can do can be negated in Aurora. This is the essence of why the AI is doomed -- you can tailor your sensors, speed, weapons, sizes, ship types, doctrine, fleet composition, and locations to exploit your enemies' weaknesses. In VB 6 Aurora the AI will not do the same against you. The proposed AI for C# Aurora will address a few of these issues, but not many.
I'm a bit discouraged to hear that spamming enough missiles get anything done and the only real limitation is that you need to build and stow them. However, with sufficiently advanced tech can you counter most missile barrages?
Missiles are tactically very strong, but strategically a huge weakness. I have defeated countless enemies by running them out of missiles (whether locally or empire-wide) and then destroying their useless hulks. It is not particularly difficult to make a ship that is
less expensive than the missiles needed* to destroy it. Indeed, the fiction sections on this sitea are full of examples of Empires shooting absurd quantities of AMMs that cost half as much as the missiles they are meant to destroy at 5v1 rates.
And again, at virtually
any tech level, you can build 'missile-proof' defenses if you know the details of the missiles you are trying to counter and design things specifically against them.
And going off that, how effective are super-fast, deadly and short ranged missiles launched from carrier-based stealth bombers from up close?
That depends strongly on how fast and how stealthy the bombers are, and how "up close" they get.
Is that a good strategy?
Is it fun for you? That is
LITERALLY the only difference between a good strategy and a bad one.
If you don't know, try it and find out. If it's mostly fun -- but annoying in ways A, B, and C -- then don't be afraid to use SpaceMaster mode to alter A, B and/or C.