Maybe it's just for consistency of pronunciation. Spelling the abbreviation 'veggies' encourages use of the soft 'j' sound. I'm a pescetarian, abbreviated to pesky, as no-one would know how to pronounce pescy.
But that's just what puzzles me - it's inconsistent. Doubling the g makes it into a hard sound when followed by i, e or y, eg bag, baggy, baggies. Gag turns into gage if you add an e. Mag turns into magi if you add an i. For consistency of pronunciation it should be veg(etables), vegy, vegies.
Pesky makes sense to the hoi polloi of non-pedants, as it's not immediately obvious that the -esce has a hard c.
It's because of a monk called Orrm who devised a way to indicate whether vowels are short or long in about 1200, and it involved doubling the consonant after them. So he would have had "veggetables" (or possibly even "veggetabbles") as well as "veggies". His relentless way of doing it ("catt", "matt" etc) didn't catch on, but the principle of using doubled consonants when there's any doubt about the pronunciation did, hence a cat purrs with two Rs, but pursues a mouse with one. And "pure" has one.
"Vegetables" comes from a Latin word whose pronunciation was already established, but "veggies", which is modern, has inherited Orrm's legacy.