It won't affect the performance at all.
You can even leave the Denise chip out, the Indivision provides a hardware level Denise replacement so it doesn't matter if the "real" Denise is OCS, ECS or even present at all as far as output from the Indivision is concerned. The only reason to keep Denise installed atop the Indivision is to keep having output from the DB23 video connector.
As a Denise replacement, the Indivision ECS is of course ECS capable, provided an ECS Agnus is also used.
Of course ECS screenmodes will only be usable via the Indivision's VGA output if the "real" Denise is OCS.
Thanks for that info, I wondered about the Denis chip and if it needed to be on there or not.