Pretty much the main thing collectors look for is that all the parts match.. The Chrysanthemums are "secondary" because so many were defaced. Mums will increase the value on a matching rifle, not so much on a non-matching one.
As for shootability, its the same as any other old mil-surp.. Look for a good bore, they have "Metford" rifling, it doesnt have the sharp lands & groves like most, but should still be sorta deep (enough to spin the bullet). Be careful for training rifles, they will have a smoothbore and are designed to shoot blanks ONLY!
There is some doubt about the "last ditch" series of Type 99 rifles. I do not know if they are safe or not, I tend to stay away from them just because they are so crude looking. (They make a Mosin look nice!
As to what type? What ever strikes your fancy.. The Type 38 is 6.5x50, the Type 99 is 7.7x58 (You can make 7.7 brass outta .30-06)
There are 3 variations of the Type 99.
The early ones have the Dust cover, Monopod, & Anti-Aircraft sights. Later in the war they came out with the "Simplified" model, as metal became sparse, they started to leave off all the "unnecessary parts" (dust cover, monopod, & Anti-Aircraft wings) They may or may not have some or all of these accessories. Finally towards the end was the "Substitute" or "Last ditch" models. They dont have any of the accessories of the previous models, the metal is crudely machined, the rear sight is fixed with no adjustments, stocks are rough and look sorta "carved", many have wooden buttplates.( Although if you can find a real late one with a rope sling, those are pretty collectible!!)
Most of my friends like the Type 38 Carbine. I personally like the early Type 99, Its like the "Tactical" rifle of WWII.
Look for one with accessories, slings, dust covers, cleaning rods, monopods. Some of that stuff is worth more than the rifle!
Best site for helping identify a Arisaka: http://www.radix.net/~bbrown/japanese_markings.html