When I lived in a 2 bedroom apartment, I wanted the second bedroom to look like a bedroom and not a bicycle storage facility. (My landlord had some issues with my bicycles) So I bought a loft bed ... it's basically the upper bunk of a bunkbed. The bed part can be set up at different heights, but I chose the highest, and then I put the bicycles underneath. I could fit 5 bicycles under there if I set them in just right.

To hide the fact that there were 5 bicycles in the apartment (actually I had 6, but one was on my trainer), I bought fabric shower curtains and hung them from the rails of the upper bunk. The bicycles were tucked neatly underneath, and at a casual glance, no one would be the wiser.

I also got various hooks that I could put over the slats, etc., and I hung my tires and some of my other cylcling stuff under there too.

In your case, if you didn't need to "hide" the bicycles under there, or create a guest room, you could also use the bunk area on top to store stuff.