Aperture won't recognise NIK plug-ins since I upgraded Aperture

Have you upgraded to Aperture 3.4.x?

Aperture is now sand-boxed and will only work with sand-boxed, 64-bit plug-ins; see:

Aperture 3.4 and later: Some third-party plug-ins are no longer compatible

Check, if you have the latest versions of your plug-ins, or if you can upgrade them to be compatible with Mt. Lion.

and when I go to use Nik plug - ins it says the developer is not a recognised provider.

Also, try, if you can run your plug-ins, if you disable the security check of the developer in the System Preferences "Security and Privacy" tab:

You will have to click the padlock and enter your admin password to make changes.

Regards

Léonie