I think all cars with roof boards were originally equipped with pans, but some of them had the pans removed within a year or two of them being delivered, and those cars were then assigned to the brown line. I guess they initially over-estimated the number of cars needed for Skokie service. Also around that time Saturday service was cut from the Yellow line, which might have something to do with it.
There are also a few pairs of cars out there which have the footings for roof boards, but no actual roof boards. I can't figure out if these initially had boards but they were removed, or they were built so that they could be skokie-equipped later on.
That old car might be worth money!