SSI Security Threat(s)?

[ZiNgA BuRgA]

SSI isn't inherently insecure.  Yes, disabling it will probably make your system more secure, just like switching your server off and never turning it on probably makes it even more secure (though not very useful).
If you're not using SSI, it's probably a good idea not to enable it is all.

As for system/exec etc calls, if there is no way for the user to directly affect the variable you're sending to the function, it's probably okay.  That's a "probably" though, there can be other factors, for example, if they can modify the underlying executable (though chances are, if they can do that, they can probably modify scripts too).