The amount of chakra required to create a vacuum, even if only for a spherical liter of volume, would be enormous. I'm not sure how proficient a character would have to be with chakra control in order to achieve such control of the atmosphere.
A better question is what effects would a vacuum have on the human body?
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From a chemistry/thermodynamics point of view we know that reducing pressure also decreases the amount of thermal energy required for liquids to evaporate, hence reducing the boiling point temperature. Due to this fact, some have hypothesized that reducing the pressure of a system to < 1 psi (= 6.895 kiloPascals = 0.06805 atmospheres) would cause a person's blood to boil. However, this doesn't seem to be the case since the internal pressure of the body holding it's self together via laminin bonds with various proteins and whatnot is present. You don't freeze immediately, regardless of how cold a vacuum would become, because the specific heat capacity of the body is fairly high. This is demonstrated by the fact that the body is composed of ~60% water, which has a relatively large heat capacity (4.184 Joules/{gram*Kelvin}). Nonetheless, the lack of suitable oxygen in the air would allow victims of such a technique to lose consciousness after a few short minutes.
Keep in mind that a complete/perfect vacuum is very difficult -- if not entirely impossible -- to generate. Laboratories have only been capable of generating partial vacuums. Hell... even outer space is only a partial vacuum. Physicists have certainly conjured the idea of a complete vacuum as an ideal system by which absolute zero Kelvin could be achieved -- among other things -- but if modern science can't do it, neither should characters in the Narutoverse.
Nonetheless, it would be an astonishing jutsu that would enable the user to negate Katon/Enton based jutsu. However, since a perfect vacuum is impossible to achieve, Raiton and sound-based jutsu would fail to be nullified entirely.