Thanks for posting, it's fun when people notice details like that.
You're right, only the newer systems use No-Intro/Redump titles on zip files. The Vault pre-dates those projects so I originally named everything myself using the title screen, but now I'm scanning each Vault nightly and renaming each ROM/ISO that changes. Some games have loads of metadata or multiple titles which looks ugly, so I'm currently favoring zips without metadata like this:
Dragon Warrior IV.zip
Dragon Warrior IV (USA).nes
I've used that naming convention for the GameCube and Wii Vaults, but for PSP I was lazy. I'd like to be consistent but nobody's ever brought it up before so it hasn't been a priority.
I prefer .zip files since beginners don't know what to do with a .7z file. .7z compresses better though so I use .zip for cartridges and .7z for discs.