As far as I know apart from that one incident a little while back (which I think was due to the hex being compiled for the wrong board) there haven’t been any cases of a hex causing damage to or bricking an Arduboy. (And I think that case also involved the lock bits not being set, I’ll check at some point.)
The chance of someone causing damage is slim since most people aren’t playing around with the pins or writing their own hardware controlling code, but overwriting EEPROM is certainly a concern.
A number of people in the past haven’t been aware of the convention of skipping the first 16 bytes, and even more people choose to write to the earliest section of EEPROM, which (depending on how good the EEPROM’s built in wear levelling mechanism is) could cause the earlier area of EEPROM to wear out quicker.
More importantly, it means a lot of games end up overwriting each other, which is why some people resort to EEPROM save/restore programs, but that has the side effect of using up EEPROM read/write cycles quicker. Granted progmem is more likely to wear down faster than EEPROM, but I for one like to be careful, so sometimes I modify games to move the EEPROM save location.
I suspect in your case you aren’t actually using EEPROM yet, but it’s something to be aware of.
Ultimately I prefer the code to be available anyway to make bug fixes quicker and to encourage more people to make their source code available for others to learn from (which is half the point of the Arduboy in the first place).