I found .bsp files in the "userdata" folder of the Steam installation folder, specifically in "userdata[ID]\620\remote\mymaps" and "userdata[ID]\ugc\referenced[multiple IDs]\mymaps" (multiple folders in "referenced"). If I were to delete those .bsp files, would it be safe for Portal 2?

Well technically I think those are just completed compiles of puzzle maker maps which you have made.
I would cut them to the desktop, launch Portal 2 and see if anything happens.

The strange thing is that there are maps created in Hammer by other people as well, specifically in "userdata[ID]\ugc\referenced[multiple IDs]\mymaps".

I could do as you suggested because I know to do that but I ask just in case someone else did the same thing to save me all the trouble.