WishList Member 2.9 (and higher) and WishList Member 3.0 (and higher) have been developed to function with WordPress Multi-Site / WordPress Multi-User site. So the recent and latest versions of WishList Member should function as expected.
When it comes to a WordPress Multi-Site / Multi-User site, each site URL would require a WishList Member license. So, each site would count as a license activation in order to handle multiple URLs in a WordPress Multi-Site / WordPress Multi-User site.
For example, the following could use a WishList Member 5-Site license in order to use WishList Member on all 5 URLs: