Not a lot of difference
You might want to describe the intended use of the array and how you intend to connect it (esata, FW800, FW400, USB).
4 Bay:
Cost - the enclosures is probably a bit less, plus you buy one less drive
Heat - one less drive means somewhat less heat is generated, but the larger enclosure may vent better, so this is probably a wash.
Noise - again, one less drive means somewhat less noise, but most of the noise probably comes from the cooling fans in the enclosure anyway, so probably another wash
5 Bay:
more drives = more options:
* use the extra drive as a hot spare for even more protection
* add the extra drive to the array for even more available storage
the math says that 5 drives support more IO than 4, but realistically you probably wouldn't be able to see the difference in general use.
* maybe additional RAID levels supported (RAID 6)