I'm gonna only answer the second question:
I don't think you are generally safe ever deleting high quality mons in this game. Most prestigers are more or less useless right NOW, but I believe that this is a "living game". I think they will continue to change up the system now and then.
Think about it: In the old system the main priority was getting a set of high cp defenders. Attackers just needed to be level 30. It was also good with a set of strong prestigers. Now you can use anything for defense and high level attackers are much more important. Prestigers are mostly useless.
If interest is to be kept in a game like this, they probably need to switch it up from time to time.
In other words: If you are strapped for space, I would delete all of the common prestigers, that are easily obtainable (Raticate, Furret, etc) and everything else that isn't high IV with great movesets. You can use them in battle first and then send them to the trainer. But I would definitely keep your prizemons. The ones with high IV's and strong movesets that you can't easily reobtain.
As for the Venusaurs, I would personally keep the 90%+'ers for now.
