Does the Arduino have any specific cooling requirements?
The only time I've ever run into a cooling issue in regards to an Arduino project was then I was running a TLC5940 LED driver chip, and I had it wired up wrong, and it melted the solderless breadboard. So, that's not even related to the Arduino directly.  I've never run or even heard of a circuit that was wired up correctly make the Arduino get even kind of warm at all.  

If your circuit runs cool to the touch and you're never ever ever ever going to need to get to it, it should be okay to encase it in epoxy. Never say never, but if things are running normally, it should be okay.

Also consider alternatives to epoxy; air/water tight cases are possible to obtain if your project is water/moisture/dirt based. If buoyancy is a concern, you can always add steel plating or lead shot in the case.