zlib is included, so in theory you can do some wrapper stuff around it. See here for writing zips:
https://github.com/koreader/koreader.../zipwriter.lua
And here is a wrapper in C that also deals with crypt/decrypt. It probably doesn't make an awful lot of sense to ship that with KOReader; at least as a first step I mean that more as inspiration to write it in LuaJIT instead.
https://github.com/zlib-ng/minizip-ng
Although fwiw some bindings for minizip already exist too:
https://github.com/luapower/minizip/
Though come to think of it, maybe you could outsource decryption to OpenSSL, which is also already included.