«Що» is 'what', «коли» is 'when'.
It makes sense because morning is a period of time. You can eat at 6 am, 7 am, 8 am, 9 am, 10 am, and all these will be «вранці». So, this question is asking when exactly.
Of coures, you can use «що» to ask about the food you eat. But it would be a different question.
"Що ти їж/їсиж вранці?" ('їси" on it's own doesn't make sense.)
In literary Ukrainian, the verb «їсти» is conjugated like this:
- я їм,
- ти їси,
- вона/він/воно їсть,
- ми їмо,
- ви їсте,
- вони їдять.
And «їж» in literary Ukrainian is an imperative, used for requests and orders.