Not a stupid question at all, IMO.
This is conjecture & speculation but I would think that Nike might (emphasize might) cut some kind of check for these athletes; after all a big chunk of the buyers are fans of the athlete, the shoe being just an accessory. It could probably go the other way as well, with the athlete's association being a side note.
(In that respect I've bought Foamposites based on how the shoe looked & felt; I could care less which NBA athlete endorsed them, I jsut thought they were cool)
If Nike is straight cold business though they would have had them sign a release or waiver form & other paperwork upon the expiration of the shoe deal stating that Nike is free to use his/her likeness/association, etc. in (insert # of years here) to continue to promote their products, with little to no monetary compensation in return. *IF* the Penny logo is owned by Penny himself, then I'd say Nike does owe him some money from the money tree that is reissuing retro models, but if Penny signed that away & that was a Nike creation (1 cent logo) then that is Nike's free & clear. Some help from the legal field NTers would come in handy right about here...
He could also be "paid" in terms of free shoes, clothing for his friends & family, input into cw options... Just some ideas for thought.