I have to admit that HDD's were also an issue for me, but putting 2 of then into the 5.25" bays along with the extra fan has really helped things a lot - I didn't want to have to use the second 3.5" bay in the middle as I think it'll make the airflow to my GPU too 'dirty' - the lack of a side fan was also a concern, but now with the extra front fan my GPU temps are almost the same as before with the Antec300. The positive pressure system of the Fortress does seem to keep dust at bay from what I've seen so far, so it's all good!
I would say that you could get up to 10 x HDD's internally if you used all 7 of the removeable 3.5" bays and 3 of the 5.25" bays as well, and that's assuming you'd only have one DVDRW drive and a fan controller (which seems to be favorite with this case).