I think that was different in 1.1 so something is wrong with the migrated code.
This is not, as far as I can tell, the case. (Or not mostly.) Comparing the last version in my 1.1 directory to now, some of the names have changed, but the stats haven't. It's -odd- IMO that not all of the fuel rods are allowed in the nuclear locomotive and that many non-nuclear fuels are, but it sure looks like that's how it was.
As far as the comparison goes, I think you may be just looking at raw stats and not taking into account fuel bonus. (And to be honest I had an entire reply written before remembering them, so you're in good company.) I don't think the disparity is quite so bad between the nuclear locomotive and the space locomotive with that factored in - the former can go nearly as fast on thorium fuel rods, though the acceleration is lower.
The EM suspension train 1, with fuel bonus, has much higher acceleration than the space locomotive regardless of fuel used, along with modestly higher speed. The locomotive is a lot heavier. I'm... honestly not sure how much of a difference that makes? I did a straightline sprint test, and using thorium fuel rods with a simultaneous start, LCC trains for both, the space train took an early lead, the suspension train pulled ahead in the middle, then came in just a little behind at the finish. With uranium fuel rods (slightly higher acceleration bonus), it's similar but almost a simultaneous finish. That's with no braking force research. BF5 seems to help the EM train a bit more, but it's not huge. I don't know if turbochargers would help one more than the other or not. (It's odd IMO that they work at all on non-diesel trains.) I don't know how likely one would be to run their trains on the superior mox or high energy mox fuel rods.
Overall... I think the nuclear locomotive is more or less okay, though if it were me I might make it available a bit earlier. (If we can make a train nuclear reactor at rocket science, why not a train that has a nuclear reactor built in?) The EM suspension train 1 suffers from it's high weight, though I don't know how much of a difference that makes in practical applications. Still, if it's to be a clear upgrade, it might stand being dialed down a bit, or possibly something else tweaked.