If you never installed them in the first place, you need not worry about them.
The thing is like this: Certain applications needs these special things - Video codecs, a Java runtime, Timidity bindings - and if you try to run them without those things in place, they won't run (or run badly). The installers copies the relevant things to the NAND (yes, these are things that need to have something in the NAND), where the applications will find them, later.
When you make a full reflash, the whole of the NAND gets returned to its original state. Which means no {Java, Timidity, codecs}. If you usually run something that needs Java, for instance, it will just no longer start. But there is no other problems - Nothing of the usual pandora functionality breaks, nothing gets damaged, and the only thing you need to do to get everything working again is slap your forehead, groan "Darn, I forgot to reinstall JAVA", and do it. There is nothing much to screw up.