Compressing a FLAC into a ZIP archive won't hurt anything. You won't save any space because the file is already compressed, but you will gain the convenience of combining several files into one.
ZIP and FLAC use the same basic technology: Lempel-Ziv compression, which encodes repeating parts of the data into a form that takes less space but can be recovered completely. Think of writing "20X0" instead of "00000000000000000000". The details are more complicated but that's the idea.
I am assuming you mean storing the folder on your hard drive in a .zip folder right? I would imagine it might save you a small amount of space, but it just adds more steps when you need to manipulate the files.