The way I understand it, they are imported or they are integrated with existing system tables, regardless of showing or hiding system tables. Having said that, I think, I believe, if you use VBA to hide the system tables, you will not be able to import them. I did some testing before and I think this was one of the results of my testing.
The way I understand it, some features that are imported rely on System Tables. So I would have to assume it is possible the Import Wizard may import information from the System Tables. The exception may be if you hide the System Tables using VBA.