I poked about looking for a EULA, I had just assumed that there was one when I paid for it as there normally is one. Revers engineering stuff is normally there, but turns out there's no EULA but there some words from Notch saying you can make your mods, just no distribution of his code. That does change things.
If I was him I'd still not be wanting to work directly with the modders as you could still get into awkward legal spots down the line should need to go after a project you had worked with (and thus approved of) for distributed the code. It's not that there's a problem with him working with them, more it could weaken his position if it ever came up.
I don't think there's any evidence of the API, you've just got to trust the developers on it. There may be some hooks added into the code itself that's released, but I don't look at that to know. We've paid for an unfinished game that my never be released, so we must be trusting them already to get the job done really.
As for transparency, it doesn't have happen until there's an API for me. Right now people are just doing whatever, and know that an API is on the way so you're asking to be bitten in my eyes.
Still, it would be great if CraftBukkit didn't have to break every week. The guy who was hosting the server I used to play on got sick of it and has given up running the server until things levelled out.