Jim -- Here are some pros and cons of extended choke tubes include:
1) extended tubes are usually easier/faster to change (no wrench needed),
2) most extended tubes identify the choke/constriction on the exposed portion where you can see it while some flush tubes don’t have notches to indicate choke constrictions,
3) extended tubes provide muzzle protection from possible muzzle damage (dint) that could make choke removal or instillation difficult,
4) extended tubes provide additional length which allows for the possibility of different choke geometry and design (ramp angle and length, choke angle and length, parallel section length, porting and endless marketing gimmicks) which may or may not provide improved performance,
5) extended tubes usually weigh more than flush tubes which may or may not be a good thing for your gun’s balance,
6) some shooters think the extended tubes look cool and some like the traditional uncluttered look of flush tubes, and
7) extended tubes are generally more expensive (the choke makers like that).
None of this means extended choke tubes work/perform "better" (whatever that means) than flush chokes. It really depends on the kind of performance you need/want from your chokes and loads for your type of hunting/shooting. However, if you aren't going to take the time to pattern them properly to find out how they really perform then it doesn't really matter, just use what you like.
Hope this helps, good luck.