Welllll first go to safari preference and tell it to stop opening archives on downloading them, its's in General. Then when it downloads pk3's it will still put .zip on the end but you can just edit this out.
So box.pk3 becomes box.pk3.zip
just change it back.
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Also to recompress pk3's I use this:
http://www.macgamefiles.com/detail.php?item=18400
To make pk3's use the jedi academy option, it works for nex idk why.
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You don't need to access dlcache to use downloaded maps in nexuiz but it is a little tidier and will stop you having duplicate files. To make ALL the hidden files on your mac visible do this in terminal:
defaults write com.apple.finder
AppleShowAllFiles TRUE
killall Finder
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Then just do a search for .dlcache
It makes all your directories look a mess and i always feel like Ima do something fatal to my mac while i got all this stuff showing. But what you can do is create an alias for dlcache that will still be visible when you hide all the dot files again, so you should only have to do it once.
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And to hide them again:
defaults write com.apple.finder
AppleShowAllFiles FALSE
killall Finder
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Last of all it is possible to make pk3's using the commandline but idk how to do this and i prefer a gui anyway. Perhaps somebody could add this?
