I know with Apache if you have an SSL certificate with an encrypted private key, you need to enter a passphrase whenever you restart the server in order to decrypt it and load the key/certificate. (Or you used to, at least.)
Does a similar thing happen on Windows with ISA/IIS and the built-in certificate store? Or, when you import a certificate does that obviate the need for entering the passphrase all the time? Does it ask when you reboot, restart IIS, etc.?
I'm trying to determine how impactful it will be and/or if I should decrypt the key...
Importing the certificate to the Windows certificate store does not require you to reenter the passphase post-import, nor reboot, restart or otherwise affect IIS. You will never be asked again, post-import.
Follow the steps here to import a certificate (iis7).
Note that you need to combine your issued certificate and unencrypted private key into a .pfx file (PKCS#12 format) in order to import it into IIS. So another way to look at it is that you can't do that at all.