Public data repositories: Multiple figures as one reference
I routinely use OSF (Open Science Framework) and have a single reference to Supplementary Materials that links to a compressed file on OSF. You can "register" (fixed snapshot) the set of materials you want and have a single reference (including doi). I don't do it quite like that, I simply refer to Supplementary Figure 3 or whatever in the paper, and provide the link in whatever way the journal requests supplementary materials be linked.

But it doesn't have to be a single compressed file. The way OSF archives work is that the single link is to something more akin to a webpage and you can have multiple files able to be downloaded as well as a wiki style information page. It would be annoying for your readers to have to download multiple files though.