They both have sports, but neither have 2 in each season, at least according to their own school websites.
Put-in-Bay's sports are coed CC, volleyball, boys and girls basketball, archery, and sailing. The last 2 not being OHSAA sponsored sports I wouldn't think count toward the 2 per season rule.
Kelley's Island has only CC.
I'd imagine that since they're special cases where the schools are tiny, the cost to send students mainland every day would be astronomical, and they don't enter OHSAA tournaments anyway, they don't enforce the rule on them. They're really just members in name alone, considering their schedules have very few actual OHSAA members on them (and in PIB's case, they have Ottawa Hill's listed for bball.....OH doesn't have the same, so it very well may be a JV game for OH anyway) and they don't bother entering the postseason.