Hi,
all that happens when you Harden the System using the ISA Security wizard is the following.
If you go for the secure option it applies the Hi Security Server or High Security Domain Controller security policy - for a complete list of EXACTLY what happens load the security template into the Security Templates MMC Snap-in.
For dedicated and limited services it loads either the Secure or Default template respectivly.
All these templates are stored in %systemroot%\security\templatesand they specify service start up, registry premissions and keys and file system security. You will have to use common sense in order to work out which policy is which (but the domain controller ones all end in DC and the Server ones end in SV).
Nothing should be uninstalled, but you may find that components such as OS2 and POSIX support are removed for you in a secure environment - they are provided for backwards compatibilty and actually reduce the security of your system.