Seeing as I keep needing models that aren't in Portal 2, I eventually caved into going into my portal .vpk and porting over almost all of the models (making sure not to grab anything already in Portal 2) into the external folders in \Portal 2\portal2., like I had done with textures previously.
The good thing is now I have a ton more models to work with, but I'm wondering if this might make releasing maps in the future harder for me. And I'm also worrying about certain things possibly being buggy.
Should I have not done this, or will I be alright?

You just have to include custom content (which isn't already provided with Portal 2) in your map .bsp file (see Pakrat). Everyone does this (at least those many people that use custom content).