Beads definitely can have a "yuck" factor.

There are two ways to go about cleanliness. One way is to use a smallish warm water enema or two before play. This reduces the likelihood of the toy getting very messy in the first place.

The second way is to take care of things after the fact. Two paper towels that can be folded over the toy can be a good way to start, then you can either wipe it off with them or slosh it around in a sink.

Scent removal is the most difficult. Silicone can be sanitized and pretty much completely cleaned, so I'd stick with that. What happens is that some smelly compounds latch onto silicone the same way that the red from tomatoes latches onto Tupperware. Removal can be hard - try soaking in a strongish hot dishwashing detergent/water mix for an hour or so. Another one that seems to work OK is certain shampoos - let it sit for a while, then rinse in hot water.