There is no problem per se from zipping or unzipping the .app or library package. It's generally a good idea. That alone won't harm the contents.
But if a single bit in the .zip file is altered by transmission errors or bit rot, unzipping can turn this minor error into major damage. This is due to an exponential chain reaction called bit error amplification. You won't notice this with Finder's built-in decompression -- until something bad happens like FCP crashing trying to open the library.
Whether the error is found or not, the file is nonetheless damaged, just in the Finder decompression case you don't know (until something bad happens), and if decompressed by The Unarchiver, you immediately know.
Years ago I tested various zip and unzip utilities and used hex editors to inject small binary errors in the zip file to verify the unzip CRC check always caught it. They seemed to.
Fast forward to last week when I repeated that test using Finder compress/decompress, and I was shocked to find Finder did not validate the checksum on decompression. If you use The Unarchiver to decompress the Finder-compressed file, it will always find the error (if present).
Storage systems are pretty good so you may never see this. Or maybe some have seen this but attributed it to a mysterious FCP bug. The benefit of validating the checksum is it tells you the zip file was damaged between the time it was compressed and the time it was decompressed.