Some types of aluminum will erode easily from urine.   Pull the mats back and check the corners.  You will see pitting and obvious thinning spots.   It is actually more important to get under the trailer and check where the aluminum floor meets the beams.   Use a flashlight and a small screwdriver to poke a bit in the dirty areas. 

The first signs of degradation of an aluminum floor will be spots of white chalky dust.  If the condition is not taken care of, these chalky spots will turn to a grey pasty material, and than the pin holes start.  This is a sign that your floor is starting to deteriorate more all the time.  When we get a trailer traded in with a floor like this, we usually acid wash it thoroughly, flushing it with a lot of water.  We than let it dry well; than spray an undercoating material over it.  We than overlay the floor with sheet alumnum, adhere it to the original floor, than spray the new sheeting also.  We than have a floor that should outlast the trailer.

Logan Coach uses Aluminum planks sprayed Vortex ( There brand of Spray in Liner)

It holds up very well, But they do include rubber mats for cushioning and I guess to protect the Spray in Liner from the horses steel shoes.  My trailer is a 2006 and if I pull the mats the floor looks like new.

The Logan method uses 6" wide aluminum planks with a 1/4" gap between the planks so any urine drains out. So it is really easy to rinse out 2-3 times a year.

quote... Several people have commented on protecting aluminum floors by spraying Rhino/Linex over rubber mats

That's the first I've ever heard of spraying truck bed liner over top of mats.... That just ain't going to work... Even if you were to use it on the floor, you will still need to cover it with the mats to keep shoes and or hooves from scraping it off, plus that bed liner offers little to no cushion to the horse...

I got trailers with bare aluminum and mats, wood with mats and aluminum with W.E.R.M.. The WERM floor gets my vote hands down.

A shod horse can tear up a bed liner material, both the professional two part hot applied, as well as the single part cold applications. The mats are installed over the liner, which should be first applied to the metal flooring. They protect the liner from the hooves. A properly applied liner will protect the flooring from moisture and air, both of which are necessary for corrosion.

Applying the bed liner material over the mats, can cause it to fail from flexing and cracking, allowing moisture and urine to penetrate its surface. Once moisture is trapped, corrosion can occur quickly.