It is a bit of a dilemma. I would try .31.08 for a bit and see if you like it better than 40D. If you do, play .31 if not, there's no harm in going back to more stable 40D.
The equipping daggers bug does seem to be fixed from my experience, and I havent gotten a crash since I started playing .08. But .08 still has it's oddities, most inorganic (and a couple specific organic) creatures are effectively unkillable without some kind of cavein, or sometimes a magma flood. And military crossbow users are completely non functional at the moment. .31 does make the underground significantly more interesting though. In 40D 90% of the world is nothing but completely featureless solid rock underground. in .31 if you dig down you are pretty much guaranteed to hit some kind of feature.
The military system is completely rewritten. So learning the old 40d military interface won't help much in the future. And you need to use the finder or have feature icons on to find anything remotely interesting underground. And you are highly unlikely to find a site where you can do everything. If there is no sand, you will not make glass. Period. No way to get the raw materiels. if there isn't a magma pipe or pool? No Magma. 40D however is more stable. And what bugs are still around are less jarring. 40D is also arguably easier to play. The underground is less dangerous, and military training is faster. And while the military interface in .31 is far more powerful, it is at least 3 times as complex as the 40D one, which might make 40d better for learning late game stuff. (If you can't work your military your chances of surviving to year 4 5 or 6 is much smaller)
So I guess each version has it's pros and cons, I would just try them both and see what you like better.