I haven't been using thought balloons or internal monologue captions in my script. I feel like the reader won't understand what's going on, or why the character does what he does. I feel like when he says what he thinks, like to other characters or something, they might think he's lying or something. Plus, I haven't really had a point to put that in.

But I kind of feel like thought balloons are... odd, or something. I feel like I shouldn't be using them. I don't know why. I'm not really going for a deep, psychological story... just the beginning of a (mostly) straightforward, somewhat shounen-like webcomic. Now that I think about it, a lot of anime I watch have the main character's thoughts spoken in the show, and some manga use some kind of way of writing down the characters' thoughts. It's only for the main character, the one who's head the reader is supposed to be in, so... I don't see why not.

I still feel like I heard somewhere that thought bubbles are bad and amateurish. Anyone know a reason someone might say that?

Naaaaaw...

Thought bubbles are fine if it works within the construct of your story and overall aesthetic. They're a little dated and considered passé by a lot of creators and readers, but I don't see any reason why they shouldn't be used. They're just a tool. Certain tools are perfect for certain jobs. If thought bubbles work, by all means, use them.