If you're doing mostly "crunch" type guitar sounds, you might not notice the difference. If you're trying for the cleanest sounds you can get, you would probably notice the difference. I say "probably", because I don't own either piece of gear (my wife probably wouldn't believe that statement)
Most mixer inputs, including the mixers in porta-DAW's, take line inputs and attenuate them to mic level, then put them thru the mic preamp and boost them back up to line level. I've always thought that this is a stupid practice compared to adding one simple switch for mic/line select, but it is still done...
Sooo, if you feed a line level signal into your porta-DAW, it will be attenuated and re-amplified, which adds noise. The input from the J-Station, which should be compatible with a guitar amp, is most likely a lower level signal than line level, and might not suffer as much from the un-necessary level conversion. Still, it seems really stupid to cut a signal so you can amplify it again...
If the J-Station has the option of full line level output, you could get nearly as good a sound by taking this line level output and plugging it into an insert point. This would bypass all the preamp stuff in the DAW.
Anybody who actually HAS one of the Yamaha 16's, feel free to chip in here if there AREN'T any inserts...
The SPDIF and optical digital signals in most gear bypass all the preamp stuff and assume that it's a line level signal. This would be the cleanest way to go for direct transfers, assuming that you can get the two to talk nice... Steve