There is NO difference between EMSurf with waveports and EMSurf_TL. Due to some legacy in our framework it was necessary to package the wave port functionality under a separate tool name.
If I remember correctly, I believe that the waveport function in EMSurf was disabled at some point. I am guessing that this is what the second question is referring to. This problem has already been corrected. If the currently downloadable version does not have waveports enabled, the function will be back in the next update.