JPRA = Jurassic Park River Adventure (aka JP: The Ride) lol
Well its a rather WET ride, so its closed during the winter/early spring months due to the chilly cold weather. Same for Roaring Rapids. If its closed on a warmer day, thats just Six Flags being cheap AF & not wanting to spend operational costs (hence their love of 1 or 2 train only operations... ugh. hate that crap). Jetstream has been open during the chilly season mostly because its a fairly "dry" water ride.
As far as the old Deja Vu space... that is still currently home to the Aftermath maze for Fright Fest. Also better known as the "Magic Mountain Cemetery"- Deja Vu's entrance/queue is still in place (complete with warning sign). As are the tower supports. The big building facades are from the old Batman stunt show, as well are a lot of the surrounding props. There's even an old "Comet" ride sign.
Yes, there is A LOT of locations around the park that could be home to a multitude of flat rides and more. The problem is, Six Flags is cheap. They're sadly delusional in thinking they are a quality destination park just because they have 19 rust-covered slightly rough coasters. The park fails to offer any form of entertainment (which people have complained about repeatedly), they hardly use their characters, and a lot of their food locations are usually closed. They only have ONE full service restaurant in the park. Only one quick service location with indoor/covered dining. Terrible plumbing issues. Magic Mountain is approaching 50 and its sad that the other 4 big name parks in CA are in better condition.