I've been renovating our new home and in doing so, removed three 220v heaters. All three are on different circuits and were (thankfully) at the end of their circuits. My issue is that I now have three live 220 12/2 wires in my attic. Can I terminate these each by wire nutting them and sticking them into their own covered (yet exposed) junction boxes?

Absolutely.

Make sure the breaker is off, wire nut them, tape the wire nuts on and then put them in covered junction boxes, plastic or metal. Personally, I would hang them somewhere so you can find them later. Go to the breaker panel, put a piece of tape over the breakers and mark the panel listing as disconnected. One good thing is that you do have 6 more spaces in the box. You can also pull the wires out of the box, tie them up into the floor joists or at least out of the way, put snap in caps in the old NMC holes. When you need expansion spaces, use the existing breaker or pull them out for 120V spaces and fill in the empty breaker panel spaces.