I have a plan with 6 HCEs (and of course several NHCEs), 3 HCEs want the 3% Nonelective and 3 HCEs want nothing at all. Do I have the flexability to exclude any HCE I want from the SH?

Yes, if your plan document allows and it is clearly written to handle it in that fashion.

I would think about restriciting all of the HCEs and then providing the 3 who want a contribution a regular NEC via a new comparability allocation. That way, the client can have that money subject to a vesting schedule and have the flexability to provide or not provide it every year.