We don't know a ton about the final design for system-to-system jumps yet, but the original concept is that you have to actively fly your ship through a somewhat twisty "jump point" wormhole thing and come out the other side. That would be long enough to cover the loading time, but it's all active gameplay instead of loading screens.
It also won't need to load the whole system when you jump in, only the "low poly" versions of planets and moons and whatever large scale spacescaping objects (gas clouds, etc.) are visible from where you come out. The more detailed versions of planets and moons only need to stream in once you pick where you're going within the system spool up your quantum drive to get there.
If you don't want a "quantum drive" scene going from one place to another, you're also free to make a seamless flight using regular engines! Port Olisar to Daymar takes a bit under 10 hours.
https://www.youtube.com/watch?v=C_iXlgxsEVc (timelapse of that trip condensed to 15 minutes)
And if you're in something bigger than a single seat fighter, you can get up and do other stuff around your ship while it's traveling, but it's not a good idea in areas with pirates. Still, more options than a Mass Effect elevator.
Flying around a planet/moon all the way down to the surface, getting out of your ship and walking around, and going inside the various outposts happens completely seamlessly. I've only fired it up a couple times since beta 3.1 came out, but my first trip down to Yela was pretty mindblowing.
There's also related work with getting things like ship spawning off the main thread and improving the networking so that it only sends you data that's relevant to areas you're in.
Hopefully this stuff doesn't get pushed further down the schedule because it should make a big difference to performance.
You can see their development roadmap online: https://robertsspaceindustries.com/roadmap/board/1-Star-Citi...
As for not being able to imagine playing any FPS at 40hz -- I grew up playing FPS on computers which really couldn't handle playing FPS, pushing "entry level" $25 nvidia cards past their limits because I wanted the pretty graphics, 40 frames per second sounds amazing when you got accustomed to 15 ;)
And 40sec of load time on an SSD? That's a lot if you ask me. Fortnite loads in <5secs, CS:GO also in <5secs. Just few days ago I installed Quake Champions and the game needs 30+secs to load and it's really frustrating, considering matches are quite fast + their menu forces you to look at all achievements and all the crap I don't care about. Waiting is horrible.
It's great hat they are making improvements, but as another commenter said it seems like they haven't polished core gameplay enough -at least not enough for me to care.