The goal of the NATO spelling alphabet is to make the symbols as easily-distinguishable as possible, even over noisy channels (such as radio). Brevity (keeping the words short) is secondary to that. So it comes down to optimization.
In the end, the original designers determined that the extra clarity from using some three-syllable words outweighed the extra time it would take to say them. It's the same reason four-syllable "affirmative" and three-syllable "negative" are used over the radio: it wouldn't be hard to come up with two-syllable or even one-syllable words for these ("yes"/"no", "confirm"/"deny"), but confusing the two could be absolutely catastrophic. So the extra certainty is worth the extra syllables.