So my husband corrects me every time I ask our 5 year old "Did you eat your food all gone?". He says I sound immature and its not proper English. So I would like advice from other mothers of young kids about how they ask if they finished their food.
If you said "Did you eat your food all up?", that would make sense in English, because "eat up" is a phrasal verb meaning to eat completely (among other meanings). Splitting "eat up" that way in the sentence has a "baby talk" quality to it, but it's grammatical.
There is no phrasal verb "eat gone", so "Did you eat your food all gone?" is strange, and sounds even more like baby talk.
So, I agree with your husband. But, I'm not a mom, so what do I know?
Note that punctuation matters here.
Did you eat your food? All gone?
These two sentences are perfectly fine by themselves. But if you parse it like a single sentence:
Did you eat your food all gone?
That is not grammatically correct.
It may be better suited to Parenting.SE to answer whether using baby talk with 5-year-olds is still okay (educationally speaking) - I'd err on the side of no but I defer to the experts.