I've never worried too much about SH contracting pathogens from established non-Syngnathids. However, besides the temp. issue, if you like the water in your "main" DT pristine, you'll be fighting that battle once the SH setup is added. SH must eat daily, and produce a lot of waste both when eating as well as defecating, so your NO3 level will be higher unless you step up the maintenance accordingly.
BTW, SH do wonderfully in macro setups...that's about as good as it gets for them.