I would have to agree in general on adding the complexity of thermodynamics, you start crossing a threshold into simulation vs game when you start throwing too many management-heavy parameters into the mix.
That said, I would NOT be opposed to very basic and general thermodynamics, keeping them very vague and non-intrusive. I'd use something like the basic heat mechanisms that games like Mechwarrior have used in the past. For example, add a heatsink block that will dispel X amount of heat (volume based), make it fairly heavy, and then tie it to just certain ship functions. The engines and thrusters are very "ion-like" so you can assume they are ejecting heat as plasma during their operation (to make it simple), and their heat impact might be minimal. Except when you have the afterburners kicked in. Then make things like weaponry, mining and salvaging, etc. generate heat. Generate too much heat, fill the heat sink bar, and weapons and afterburners are unavailable until cooldown is achieved. Something along those lines, with it staying basic and having a risk/loss weight when deciding if you want to add sinks, could add a little finesse to ship building.
Anyhow, that's my thought... I think it could add some depth, just have to be careful that you don't dive too deep and scare off people that can't swim well. ;)