Yes, it’s true that some pokémon actually differ in composition from the more traditional carbon-based class. However, it’s a bit more complicated than one might think.
To be a bit more specific, only very certain pokémon under very particular conditions are silicon-based. It’s true that many of these are rock- or ground-types, but in addition, they’re not the ones that have even trace amounts of tissue. Putting it another way, if a pokémon possesses flesh-based organs, then it’s actually a mostly carbon-based life form. This includes pokémon such as geodude and onix. Likewise, steel-types such as probopass or the beldum line are actually quite literally steel and are thus also both iron- and carbon-based.
When you get into species that have either extraterrestrial or manmade origins or that are solid rock—such as solrock, lunatone, the baltoy line, and the roggenrola line—then you begin to encounter silicon-based life. It is also said that, being literal embodiments of their respective elements, legendaries such as Zygarde, Regirock, and Landorus are all silicon-based as well, even though one of them, Landorus, is apparently made of flesh. The exception to this rule is Diancie, as it is a living diamond and is thus carbon-based.
Then you have sableye, which eats rocks to the point where much of its body is pure precious stone, despite it not possessing the elemental affinity for the rock-type. (Although to be fair, whether or not it’s considered a silicon-based life form depends entirely on what gems comprise its diet, so whether or not it counts is up for debate.)
The Pokédex According to Bill 