from what i have monitored with signaltap, they indicate which byte is realy valid.
for example if your slave is 8 bit wide and is attached as a memory so a 32bit from nios side is 4 accesses to your slave
if your application reads the lower 16bit then byteenable[] indicate with 0x3 that the lower 2 bytes are requested. the avalon switchfabric will read the full 4 bytes.
you can add a logic between avalon and your slave that monitors which bytes are realy requested and discrads the other to get rid of these unneeded reads.
the byteenable to not mask anything they just indicated which and how many bytes of the actuall 32 databits are valid / requested.
so they are only some kind of informational.
it's up to you to use them