From what I know, FileMaker Pro and Go both use any fonts that's loaded on the machine. For FM Go its fixed fonts so that should work. Even if they don't put them on the El Capitan Font Book, you could just manually download them and install them on your computer.
I used Avenir Next once on a solution and one computer that was connecting was Windows which didn't have them on. It substituted them with Arial if I remember correctly. Avenir Next is proprietary Apple fonts so its not easy to get them on Windows and I just switched font family entirely.
A superb feature would be of course....font embedding! It may grow the file a bit but certainly bring better experience cross platform.
One more thing, WebDirect only uses a small range of web safe fonts. Keep that in mind as well.
Jake and velistar,
Now that El Cap is out, you've probably noticed that San Francisco is not exposed as a user-accessible font. Even downloading and installing the font from Apple's Developer site comes with a EULA that places limits on its use. Seems that Apple is keeping tight reigns on its use as a system font. (I'm sure they spent a lot of money developing it for that purpose, so hard to blame them for wanting to avoid dilution of the brand identity the font confers.) See the links I posted here for a lot more background.
Apple does appear to allow calling "-apple-system" font in css-styled content, however (more info at above link). Well, hey, FileMaker layouts are now composed of "css-styled content," so there's always hope that that capability will be exposed to us in a future release. I think being able to incorporate San Francisco, through allowed channels, would contribute immensely to professional looking solutions, particularly in Go, but also in desktop solutions running on OS X. You can add your votes for this feature request at the above link, if so inclined.
Certainly mark_scott Apple has spent some money on these fonts which are great. I added my vote to your feature request and hopefully will be added sometime in the future. Being an Apple subsidiary, I would have hoped to have the same fonts for use by FileMaker across Mac, iOS and Win.