Nice to see there are still people playing this game nowadays.
That said, the PSN versions are notoriously bad ports. You really did yourself a disfavor by playing the Vita version. They were outsourced to a company called Green Hill Studios and developed on an entirely different engine. And it's clear that something went seriously wrong during their development. Not only did they make numerous mistakes when porting the game, but their partnership with Nifflas was terminated after release for unknown reasons. As a result these versions were never updated to fix their bugs and add all the content that was added later.
It would be interesting to hear what caused things to end up like this, but judging by what little Nifflas has said about the matter, he's probably unable to go into details due to NDAs. All we do know is that he himself is unhappy with how these versions ended up, but has no way to update them. There are some vague hints that the game's publisher, Ripstone, played a role in this as well, but nothing concrete.
And they really are missing a lot of secret content, including some of the best parts of the game. Luckily, most (though not all) of the content you missed out on is easy to access if you know how to get it. If you want to know how, nearly all of it is hidden in the menu.
To my knowledge, there are only a handful of features exclusive to the PSN versions.
The first one is an extra room in the menu for managing the cloud.
The second is that it informs you whenever you activate a new save point. Once you've activated enough of them, you unlock one of three mini chapters you can then access via save points. These mini chapters were later added to the PC version (the Wii U version didn't exist yet at the time, but also got them), though the way they're accessed is different.
The third is a coordinate system for the map to help with navigation. Technically, it doesn't count as exclusive since the Wii U version would later get one as well, though the PC version never did.
And the last exclusive feature I'm aware of is a quest list. Doesn't strike me as particularly useful, though.
If you pay close attention to the stories of Saira and KU, it should be pretty obvious they both take place in the same universe. A few parts of Saira clearly imply that the humans in its story are descended from those who fled to outer space after the Great War. Plus, one of the game's endings contains very obvious references to WaDF and Knytt.
KU doesn't directly reference Saira very much, but that's because the events of that game happened only a decade or two before KU. Plus, it's made clear that no human ever made contact with the knytt society that formed beneath the Earth's surface. They probably don't expect anything to have survived the radiation. So even if Saira's story were to be passed along in human society, it would have no way of reaching the knytt on Earth.
There is a single reference to Saira in the game, but you wouldn't notice it unless you read Nifflas' explanation. Basically,Saira and Bobo ended up in a parallel dimension which shares the same environments as the normal one, but seems to lack any sentient life. When they landed on Earth to do some experiments in Dr. Cliché's lab, they didn't encounter any knytt due to being in a different dimension. However, by activating the machines, they also activated them in the normal dimension, which is what forced the residents of Cilia's hometown Medina to leave.