I thought about doing this myself.
You'll need an aqua box with a soft front, so that you can use the buttons and the touch screen - that may well make it difficult to read, you might have problems with waterproofing, and it'll be more expensive.
From experience with my PDA in the top of my tankbag, ventilation is likely to be a problem as well: with the screen at full brightness, in the sun, and with no ventilation, the screen would go very dull and almost unreadable until I turned the PDA off and allowed it to cool down. Car satnavs are designed to work in hot environments, but not in sealed boxes, so you may well have the same problem. You'll need ventilation in the box, but it can't let water in.
And finally, you will need to get any cables into the box with a degree of waterproofing, so you will probably have to bring them in from underneath and have the connectors inside - that makes for a pretty big box. I have also found that the connectors on PDAs don't like vibration, as I've destroyed 2 now. The last one was a mini-USB, which I thought would be fine, but it only took a couple of hours before it started to show problems.
You'll want to mount the satnav in the box with a degree of shock absorbency - as you're unlikely to find a custom mounting, try making something up with bathroom silicone. You should be able to get it in just the right place and, with the right shaping, should give you a mounting that you can release and reattach.
After considering all that lot, I gave in and bought a secondhand Zumo 500, because the cheap DIY solution was starting to factor in nearly as expensive as the secondhand option, if I wanted it to be as well engineered.