I believe the small spike in ammonia comes from the ammonia produced by the waste and uneaten food that goes under the gravel. That ammonia gets trapped under the gravel and will not be registered when you test your water normally. But when you vacuum the gravel, it comes out (never seen bubbles going up the hose while vacuuming?).
Usually I make my fish fast for a day just after a water change / gravel clean up. This decreases the load on my filters, giving them time enough to deal with the extra ammonia. I also add a strong powerhead with a venturi to really aerate the water - again to get rid of the ammonia, this time by displacement.
All in all, I vacuum the gravel once a week (along with my weekly 80% water change). And considering the amount of crap coming out when I do that, I can't think of not doing it!