Players can get as creative as they want. They typically do have counters for Web. Unless the DM is metagaming though, your average monster won't. There are spells that are more effective against players than monsters (save or die), but Web is the reverse. I'd be very surprised to discover a Rust Monster carrying a torch or vial of acid in its back pocket, for example.
If I have to give all of my monsters a common counter to a specific spell, chances are that spell is broken.
So your argument for why the crafting feats are balanced is that the DM contrive to prevent players from using them under reasonable circumstances? I'm sorry, but that strikes me as unreasonable.
It's like saying that a monster that's vastly overpowered for its CR is okay because the DM should know never to use it, except in the most unique circumstances. Well, no, any inexperienced DM is going to have to find that out the hard way because there's nothing in any of the books to even suggest that.
3e, in particular, was designed to be flexible. NPCs are often designed with class levels. Are NPCs similarly going to hold back because they want to uphold this spirit of cooperation? I'm pretty sure that there are plenty of killer DMs out there who would object to that idea.
A party of martial characters going against a party of casters would get creamed in 3e (after the first few levels, and maybe even then). Sure, they might get one or two of the casters, but it only takes one caster to destroy the entire team of martial characters. You can't say the same about the martial characters.
I really don't understand why people are against the idea of balance. It is not synonymous with homogeneity, which I could understand taking issue with. I'm not saying that things need to be balanced to the point where two classes are indistinguishable. I am saying that it should be balanced to a higher standard than 3e was.