I have to make cupcakes for a wedding. They will be covered in buttercream and then have fondant flowers and hearts on top. I did a test and the problem is when I put the fondant flowers on and then cover the cupcakes in an airtight container, the flowers literally wilted. My question is how long can cupcakes sit out uncovered without getting stale and dry?

When I make cupcakes w/ flowers I usually make the flowers with either a 50/50 fondant gumpaste mix or all gumpaste depending on the flower. Make and frost cupcakes then I usually add the flowers on the morning of the event. With the flowers all made ahead of time it shouldn't take too long.

When you keep them in an airtight container it traps the moisture and makes the fondant soft. If the decorations have to be done the day before store them in a bakery box overnight. The best bet is to do the gumpaste and fondant 50/50 mix.

Generally cupcakes are made 24 hours prior to the event. They really don't keep well like cake, even if you completely cover them and seal in the cake with buttercream or fondant.

Cakes last better on the counter because they have been completely covered with buttercream or fondant or ganache which acts just like plastic wrap to "seal in" freshness.

A solution may be to bake all your cupcakes and FREEZE them.
Make all your fondant/gum paste decorations way ahead of time (weeks or months) and store them in a NON-airtight, cardboard box.
Make your buttercream and FREEZE it.

Stage your working area the night before, take everything out to thaw (or thaw in refrigerator then a couple of hours on counter in morning). Assemble everything.
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If you haven't frozen cupcakes/buttercream before, try it out with a sample batch and see what you think.
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p.s. NEVER put fondant decos on top of whipped cream icing. It will melt into a gooey, ugly mess.