How do you remove water spots from silicone items?

Had no problem with spots. But since you're raising silicone maintenance (implicitly), I have had problems removing odors.
You want to use something that is both effective and safe for humans. Suggestions include baking soda, vinegar, denture cleaner, dilute bleach, degreaser and freezing (alone or in combo with the others).
I've used the b soda, vinegar, dilute bleach solutions at different times and found they worked.

Instead of Jet Dry rinse, I use white vinegar in my dishwasher.