I have a plywood floor covered in linoleum. I just got the vinal from home depot. Be sure to get the stuff that is waterproof on both sides, since water is at some time going to get under it. Don't be tempted to by the cheap one-sided waterproof stuff!
We nailed our on around the edges using baseboards. No glue. That way I can rip out the base boards and take it out in need be. Be sure to have it come up a good foot to compensate for bedding levels. I can post pics of ours if you want.
Also, buy the most un-textured stuff that there is, since big cracks hold in dirt.
I have only have my floor for 9 months, so I can't tell you the long term benefits. But when I cleaned the coop out this fall it was quite easy to clean and disinfect.
I found that resin also works well. I resined my other coop on the floor and 12 inches up the wall. Although it takes longer to install, it has the benefit of no being able to have water seep between it and the wall.
Good luck!