Yep a lot of mods have their sources included and bsa does include sources by default when they are made through the CK
Keep them secret? Haha, who would want that? I mean, sure, if your mod contains a 7000 line script that you spent 4 months writing, I could understand keeping that secret. But if your mod contains a large amount of 1-30 line scripts for doing things around, why? I plan on including my source files when Falskaar is released. I just have to remember to include them!

But, yes, unfortunately some people dont want to show their sources. Even If you ask.
Anyway, I have one rules for myself: never run those mods.
I want to check if the scripts are safe and if the coder knows what he is doing. I got too many troubles with some badly coded scripts.
Skyrim is a very open game, we can change anything, I dont see one single reason for a mod to be closed.