OK ... here's the straight skinny on silicone use for seals (Ray's deviate on OS Systems first law).
Pure silicone is an excellent preservative for rubber products. It will work great on your seals and any rubber items that you own in that it seals the surface pores against air (and the rubber eating ozone in the air).
Now, that said, it is very hard to find pure silicone. Most sprays or oils use a carrier or thinner that CAN damage rubber. For example, WD-40 is a silicone product, but has kerosene as a carrier so it dissolves rubber. Many (not all) of the dive industry spray silicones are a food grade (which is safe on your latex) but doesn't use a food grade carrier.
I have been recommending using silicone grease/gel for years. It is cheap, easy to carry and isn't thinned down with anything.
The next best product is silicone oil. However, the only distributor in the diving industry of the stuff seems to be constantly thinning it down (to make more profit, I assume) so I moved it from first place to second.
There are also several silicone pump sprays that use a water carrier. It takes a lot more to do the trick (messy) but it works OK.
The most important thing you can do for your seals before applying silicone is to wash with soap and water. Applying silicone over a contaminated seal can actually accelerate the decomposition of the rubber.
Now, the biggest reason that other manufacturers say NO to silicone is that their glues are softened by the stuff. Additionally, it takes a bit more effort to clean up a repair site on suits that use silicone and some companies just aren't going to spend the extra time.
Now, all THAT said, it is best to use what your suit manufacturer recommends and ignore the rest of us.
Just my $.02
Ray Contreras
OS Systems Drysuits