There is plenty of space to get heat or toxic protection once you reach endgame where (spoilers): 1 Stun gun, 1 Anti Gravity Thruster, 1 heat shield mk3, 1 or 2 corrosion protection mk2, and 1 atmospheric stabilizer is all you need. Total: 5 or 6 and you could add lander cargo space optionally, which does all fit on your ship.
But it would be nice to also have space to add the lander combat modules too (spoilers): (armor, crew, and super-charger).
Also, I mined too much at the beginning of the game and got bored. It is better to find all those ice worlds for the Mu'Kay first thing in the game that earns you lots of RU (2000 each) while also mining what you can from those places.
Also all you have to do to get endgame heat, toxic, and atmospheric protection is visit enough starbases, which does not take long to travel through hyperspace and fuel is free since you can refuel at colonies or (spoiler): get rescued at zero fuel