I know I'm quite late with the answer but:
Vita has multiple layers of different encryptions:
1. PKG encryption -> both pkg2zip and pkg_dec can decrypt and extract those just fine
2. pfs encryption -> you can decrypt files through PC tools (cant recall the name, sorry) or through vitashell
3. eboot encryption -> We still did not get a way to decrypt those, but any modifications to it can be done in vita's memory. In case of resolution hacks you can try ren's plugin (again, cant recall the name, sorry) or use game hacking plugin (I know chinese one work with nonpdrm and retail titles) via modifying game's binary on the fly.
The reason why vitamin and maitool could create decrypted eboots is simple: They didnt use original encrypted eboot at all, they simply dumped it from vita memory. That's the reason why games with elaborated or dynamic code couldnt be properly dumped with those tools.