Nav will not let you or any program (not even Windows) access them when they are in quarantine. And as I said, generally speaking zip files are not utilized by running programs. The only exception I am familiar with is the java files installed with Virtual Machine (and this would only be the case if they were in the windows\java directory. Example: 6tzdr9zj.zip in c:\windows\java\packages)
If all your programs are running normally with them in quarantine, you should be able to have Nav delete them without any problems, but if they are a part of the java packages, you will need to reinstall Virtual Machine, one way or the other.