Not to mention the fact that if people can't see your code it strongly makes it look like you have something to hide.

This is not entirely accurate. Can you see the source for Windows? No. Can you see the source for mIRC? No. Are both trustworthy? Yes (Arguably). Do many scripts that make no attempt to hide code contain war/trojans, etc? Yes, definitely.

It comes down to one thing. Don't get anything open or closed source unless you make sure you know what it does and why.