The rationale behind wormholes being invisible until the proper research has been accomplished is the following: exploration doesn't end when you've reached a system, and goes on until later stages of the game. 

I like it this way. It has the potential to shake up the game, when you eventually discover a wormhole that could be a threat behind your border, or an opportunity elsewhere. It also fits the 4X theme; that there are things out there you can't discover until you've tech'd up far enough. 

The description of Casimir effect in the tech tree is a little confusing. It says that it "enables the fabric of space-time to be ripped open," which sounds like something you could do on demand from any location, like the Wormhole travel method in Stellaris. The fact that it's about discovering pre-existing wormholes should be more clear in the tech description, at least for the benefit of newbies to the game. Something like "Our scientists have theories that predict the existence of wormholes, this technology should allow us to discover and exploit them." Or similar text.

The back door worm holes sound delightfully evil. I would love that to be added into the game.

Food for thought, but how about having standard worm holes become visible when reaching a certain tech era (similar to how system levels are unlocked), but still needing to research a tech on how to actually travel through them. Seems like it might be a good compromise between ES1 style worm holes and what you're trying to accomplish with the new system.