if its a neck through, or a set neck where the heel goes sufficiently deep then it shouldnt be a problem, but will feel different. ensure that the bridge is well anchored, and you want as little extra length of string beyond the saddles (bridge and nut). the reason people say that a neck through body is best is that the pull of the strings holds the bridge tight to the body. extra string beyond the saddles is bad, as that means there is more string to stretch, but still the same scale length and same tension.
a stiff neck may be a good option as well (so narrow neck without much meat on it probably wouldnt be good). maybe some carbon fibre rods too.
bolt on necks dampen things, as the neck is not as mechanically sound. this makes for a good sound on longer scales, as there is sufficient presence in the attack but it decays fairly quick, making the pluck's (finger or pick) sound separated. gives a nice thump sound. i feel that by using shorter scale lengths, and using stiffer neck joints you can get a similar effect, and possibly sound more organic, as varible dampeners (bolt on neck in this case) are removed.
the second part of the last paragraph is opinion, but having less string outside of the scale length is physics.\
edit: try it by downtuning a 34" scale 5er, and use a capo on the first fret. should give you a relative sound. the things i mentioned above are just ways of improving flaws (flaws that create desireable results in some situations, so really just design features). you can only improve things so much, and shortening the scale too much will make anything floppy.