What size of tile are you using?
What size of notch trowel are you using?
Durock cement board is very inconsistent at the tapered edges. Even without the tape and thinset there can be pronounced ridges.
If a liguid waterproof membrane is not being applied I personally don't tape and premortar the joints. Apply the tape first and it gets embedded as you install.
Your setting bed of thinset should compensate for any small irregularities. If it seems too much, take a rub stone and try to remove some of the excess thinset.
You will probably be fine unless the high areas are 1/8" or more.
_________________________
Randall