I've got a '69 fish and I'd be willing to bet it has spent most of its' life, right side up. It's just fine and foam blocks still intact. I think it is probably best upside down given a choice, but I'd say do what's easiest and try to support it best you can, on the bottom of the hull, especially on a trailer. Don't worry, be happy :-D
Storing upright is fine. Just make sure to support it evenly and keep water out of the cockpit. Store it under cover and/or invest in a good cover. If water fills the entire cockpit it can leak inside the hull through vent holes or possibly through the upper seam of the cockpit.
Owned both types, upright and upside down storage. Much prefer upside down as the upright Sunfish I'm completing has a heavily oxidized deck from sunlight. I also have a 16 foot Runabout that is heavily oxidized. Can't buff deep enough to get the oxidization out. I don't mind painting the bottom and buffing the top since I like the shiny side up look. Also storing upright results in water and crap in the tub so now my tub is half brown and half faded white. Only thing worse is upside-down on the ground with no blocks under the hull. Gel-Coat becomes a total loss. If you can always store your boat indoors and it sort of become a like a bug in amber. Check all the craigslist free boat listing to see what happens to boats left to the elements.
Every time I store my fish upside down I end up with a birds nest in the cockpit storage area. My preference is right side up with a good cover. In the winter I add a tennis ball in the mast hole to keep any water from gathering and freezing. Occasionally I stand the Sunfish on the side and lean it against my storage shed when I'm using my trailer for kayaks. I haven't seen any ill effects from any of the three ways. I do use a trailer with good bunk support to keep the weight distributed.
Deck-down, building a tent/tarp but be sure that it doesn't touch the hull no moist to prevent osmoses). Inspection ports? Open and 'block' it off with -what's called I think- a piece of lanai screening material.
Normally, our boat goes into storage from November up until Late February, early March*). That's the moment we all - sailing nomads as we are- head down from The Netherlands to the Côte d'Azur/Bandol for the first training week of the season. The boat is stored upside down on the trailer, under a car port-ish construction. I leave all covers off. I prefer an afternoon polishing instead of finding osmoses on the hull.
This year, the boat will be next to my house because the final weekend sailing is at the end of November and on Jan 2, my son and his mates will be off to Vilamoura in Portugal for a 10-day training. The boats and stuff will be transported by a lorry loaned from the Dutch Olympic Committee, the sailors go by plane with only their personals.
*) I live close to the Royal Palace here in town. The boat is stored on the premises of the Palace: on the grounds of the greenkeeper & landscaper who works and lives there. I can safely say that my boat is the well-guarded. Guarded by the Military Police Guards of the Palace & grounds. Collecting the boat needs some planning and phone calls in advance. But that's never a problem.
I've got one inspection port cover that was manufactured with a fiberglass screen. Its frame is some kind of very flexible silicone-rubber, and just pops in—using friction to hold it. It's kind of useless as it's only 3-inches (maybe 4-) in diameter.