This is such an unspecific question that there is no answer to it. Last I recall, Jira was an issue tracking system, not a password manager, so you will have to broaden that question up quite a lot.
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I don't see why Jira would care whether the zip is or isn't password protected - it should not be trying to unzip it. At most, it can attempt to compress it even further, in which case it wouldn't matter what the zip contents are, because it's not trying to read it. I don't know exactly how zipping works on byte level, but I'm pretty sure it isn't reading the file. You can test it by creating a password protected zip, and then trying to make another zip/7z/jar whatever out of the file, and it will work.
So again, you need to broaden that question up because saying that something doesn't work is meaningless on it's own. We don't know if anything else doesn't work, if something else does work, if it works for person A but doesn't work for person B. I sincerely doubt this has anything to do with password protection to begin with.
If there is something akin to "you cannot upload password protected files" restriction, then I'm unaware of it.
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