Clearing the System Cache won't wipe out your photos or messages, that kind of stuff is stored in directories that you have full access to. The System Cache is its own partition on your phone's internal storage and unless you root your phone and then actually look for it, normally you won't even see it. For the most part, the Android operating system uses and maintains the System Cache, in some situations it helps to manually clear the System Cache if your phone is acting strangely (some cached file gets corrupted and screws up some function) but otherwise, just leave it as is.