I never have but would do if I felt it necessary.
I think it would be a 'disallowed modification' from a grading point of view though (but it would need to be a BKA / JKA approved kendama in the first place if this was an issue).
Off the top of my head I can't remember which but one if the common makes comes with a pretty short spike - anyone recall what I'm thinking of?
Overall, if anything for me I find the opposite issue to be more of a problem (I.E. Sara-do getting too far down) but a sliver of masking tape under the Sara-do fixes this anyway.
The advantage of both is that no single kendama is best for all tricks that's why having a few different ones is always a good idea.
My advice (if you want it) is: just play with it until it wears in naturally.