Founders totals count in clan ops provided they finish in the top 6 of their respective clan for a specified op. Essentially they are premium members with founder status.

The only way that their stats would not count in an op is if they were not a member of the clan at the time the clan was enlisted for the op.

Example: A clan leader enlists their clan in an op on Wednesday, a member with founder status joins the clan on Thursday, the founder that joined the clan on Thursday would not have their stats count for the op that the clan was enlisted in on Wednesday.