Relevant code, I think: https://github.com/cognitect/transit-js/blob/master/src/com/cognitect/transit/handlers.js#L126-L128

Encoding {1.5: 3.14} results in (verbosely) "{\"~i1.5\":3.14}", instead of "{\"~d1.5\":3.14}", so it round-trips to {1: 3.14}.

I think a fix would just involve setting the tag above based on whether the Number is an int. Naturally JavaScript has no built-in way to do this, though. I'm not much of a JS guy, but maybe Math.round(x) === x would do?