There should be no problem. The alert that macOS puts up is just a warning. None of the underlying APIs have changed. From what I can glean from Apple, 32 bit apps will still work under the next version of macOS, but with some possible issues.
In any case, I am pretty sure that Wolfram will have released Mathematica 12 before then. You might want to think about upgrading to version 12 when it comes out.