[Chris is me]

Plenty of ways to do this. The hassle of retaining on hex is way worth it compared to the hassle of dealing with keys.

Easiest way to do this is to design parts such that the distance between your bearings is exactly as much space as you need (or a hair more). You see this on things like AM / Vex gearboxes. Hex spacers work on the same principle for longer spans.

You can also use shaft collars which are a nice no machining solution. The Vex hex collars are nice, small, easy to use, and convenient. Honestly in a lot of places I don't even bother designing in spacers / snap rings anymore; the collars are that cool.

Snap rings are awesome, definitely the lightest way to retain stuff, but don't put them between loads. You're just weakening your shaft significantly when you do that. On the ends it's more than fine.

You can drill and tap the ends out to use a screw and washer to retain stuff. You may need a spacer to press against the washer.

Something else to keep in mind is that you'll also want to retain the hex shaft itself in place. Lots of these methods are more tailored for that purpose. One good way to retain the hex shaft is to turn the ends round and support the shaft with round bearings. Again, check out the Toughbox for a good example of this. You can even buy 3/8 hex with round ends from AndyMark, ready to drop in exactly two Vex or AM gears.