My mother uses a raised bathroom seat, to make it easier to get up and down, but no matter how much I scrub, it still smells horrible. Any advice?

The smell is probably from residue left between the toilet and the raised seat.
What I did with my mom's raised seat, was to apply silicone caulk generously between toilet and seat, then bolt it down.
Clean the excess silicone the oozes from the sides well before using.

I did mine when first installed, so you'll have to thoroughly clean all surfaces and dry them if you are going to do it after being used already.

Make sure to use 100% silicone rated for bath use. A big tube is around $7 to $8.

My MIL had one like CM is talking about were its bolted down. We used her bathroom on one visit and all I could smell was urine. I found that somehow she had peed between the toilet bowl edge and the highriser. I know, I could have had my husband unbolt it but I just got my hand between the two things and wiped good with the bathroom cleaner she used. I liked the bolt down idea so when I needed to buy one for Mom, I was able to find one that hinged for easier cleaning on the internet.

If you are talking about one that just comes off and on, I never found a problem with them. Where I worked had a loan closet. I was responsible for making sure the equipment was clean before storing. We had a cleaner that EMTs used to clean down ambulances. Its has no bleach. I researched, and they are called biohazard cleaners. Seems sold on Amazon. But, I would think cleaning in bleach would work. Maybe taking outside and scrubbing down and let it Sun dry. Maybe give it a good soak. 10 parts water to 1 part bleach should kill any germs.

If it's the type that is fixed to the bowl rim with clamps, you might want to take it off from time to time and clean underneath as well.

Ask an OT to have a look. There are several different types of seats and frames to help people stand and sit more easily and it could be you'll find one that is better for her and easier to keep fresh.

You may want to disinfect the floor thoroughly around the toilet as well as the seat.

Try slatering the thing in a paste made of baking soda and a little water and sticking it in the sun for as long as you can manage.

I'm amazed at how well baking soda gets smells out of plastic.

Exactly what kind of seat are you referring to? What material is it made from? What cleaning products are you using?

Are you sure it’s the seat? Could the smell be from somewhere else in the room?