The safe shallows thermals is barely warm enough to generate power at the height the Cyclops can fit into. The location you're charging it at isn't the ideal location.
It's meant to extend a Cyclop's operation time, not make it totally unlimited. Thing is, ion power cells have 5x the capacity, so if I'm not mistaken charging it to full is going to take 5x longer. Yes, it's going to be 'slow' because it charges energy at the same rate as it does normal power cells. Though I should point out I don't use ion cells on my cyclops. Better off taking extra storage or something, in my opinion.
If you're carting it around in your cyclops that's fitted with a thermal reactor, not needed. So essentially thermal reactor on cyclops = ABSOLUTELY, thermal reactor on prawn = situational - if the prawn is operating independently for extended periods, yeah, it's good. However, if I'm taking my prawn into the jellyshroom caves to pick up some of the resources down there, I'm probably going to want a thermal reactor. The prawn thermal reactor, on the other hand, eh, I find I didn't really need it if the prawn is based out of my cyclops with the thermal reactor topping it up on docking.