What will hurt your stock trailer and floor more than anything is not washing it out after use and removing every bit of urine and feces that you can. If you have mats remove them, wash them and let the floor dry out good then you can replace. The urine and feces are highly corrosive to the steel if it is not removed. My stock trailer has only needed the floor replace twice since it was new in 1987. When I replaced it I used pressure treated wood and it resists rot very well. Maintenance goes along way toward making things last. My LQ horse trailer has an aluminum floor with rubber mats over it. I still remove the mats periodically and thoroughly clean mats and floor and let them dry before replacing even though it has windows and vents that let it close up completely.