Where are the bolts located that had the rust?

I find that anything that is steel will show some surface rust after 5 years.  I go around my trailer each spring and light wire brush off rust and recoat those areas with paint.  On my Logan that areas seem to be the Gooseneck hitch and the jack areas and down under the trailer where the Dexter Axles attach to the frame. They are exposed steel show the surface rust.

Most of my Logan is an aluminum skin over a steel frame. So very little can show rust.

As far as the rivet.  Yes mine has popped a rivet or two. mostly on the trim piece between the two different colored sheets of aluminum. I've just inserted a new pop rivet.  I guess I just expect to loose a few rivets over the years driving down the dirt rides I travel.

Any trailer is going to need a little maintenance each year. Lights burn out and need to be replaced. Locks, latches and hinges all need to be lubricated.  Bearings need to be lubed and brakes replaced. Some of the padding on my dividers is showing wear, I guess thats ok after having horses rub or lean on it for 5 years.

Mine is a 2006 Logan XTR, so about the same age as what you are looking at.  If you want to detail what bolts are rusting, I'd be happy to go look at mine and see if I have the same problem. Utah, uses a fair amount of salt on the roads in the winter, and I frequently haul out to Antelope Island in the Great Salt Laked during the winter months. So my trailer does get its annual bath of salt, and I really can't complain about it being a rust bucket.

The rivets are easy to replace,  Just need the right size rivet and a pop rivet tool.  Insert the new rivet, squeeze the handle until it POP's and you are done.

I do have the Wiz Proof floor.  It has the aluminum planks that have the diagnol edges that allow any water to drain down and out.  These planks are coated in the Vortex spray on liner that Logan uses. It also has the rubber mats that provide traction and cushioning for the horses.  When I pull the mats a couple of times a year to hose out the floor,  my floor still looks new.

Logan Coach was bought out ( I think spring of 2009) So I can't speak for any changes that they have made under the new ownership.  Their XT and XTR line of trailers seem to include most items that trailer owners would add.  They came with all the small dodads that folks seem to add after the purchase. a Hose, water tank, manure fork, hat racks, jiffy jack, spare tire,  Drops windows all around, Jail bars for horse face and face nets over the jail bars.

If you are talking about the bolts that hold the rubber bumper into the steel frame. Yes, I suspect mine have some rust. But they are under the trailer body and not going to let rust stains run down the side.  Heck I just looked under my new 2011 Ford F350  I've got bolts on that frame that are only 6 months old that are showing rust. So not uncommon.  I'm sure if you look around the running gear, Where the axles attach to the frame, the spring shackles etc will all have some surface rust.