Thinking of adding some tilt blocks to the lineup as well? 

If there is not an "aspect" reason the have a box, I would personally stick with a traditional counter as I prefer those to even the tent style ones. Honestly, if you did a PDF with lots and lots topside artwork, preferably some nice scalable vector graphics, in lots of different flavors and styles of ships I would buy that and make my own counters. I can crank something like that out on demand faster than I can assemble box miniatures. Years ago I dabbled with Attack Vector and made some "box minis" with some trim wood a can of spray primer and a couple of felt tip pens and I liked the feel of those a lot better than paper and card box minis.

Any possibility you might package a boatload of printable artwork for lots of factions even if you do some other kind of counter?
Cheers,
Erik

Flat hex counters are the most ideal solution for cheap ship counters. As box or triangle counters can be hard to store, as you have to put them in a large plastic container instead of ziplock bags. Because box and triangle counters can be easily squished or broken if stored in bags.

Also flat hex counters tend to be printed on heavy duty cardboard so as such don't get blown around easily, they stack more easily and they take up the entire hex space without going over the edge of the hex so the playing field looks nice and organized.

When I was making my Generic Square Counters I went with squares over hexes simply because square counters are easier to cut out and glue on to cardboard then hex counters (And I'm not a graphic artist so anything that made it easier for me the better).