They will or at least should* let you go, work permits are evidence of legal presence in US (ex. pending family/work petition (C9), OPT (C3 A-C) after expiration of student visa, Deferred Action (C14, C33), TPS (A12, A19).

We had people pass through checkpoints with their EADs already. They might ask how you got it, just tell them it's from deferred action for childhood arrivals, they should just wave you through. Carrying the DACA letter isn't necessary, the unique category code (C33) already implies DACA.

* - There were cases of fuckers from ICE even deporting born US citizens.

Also under 8CFR 1.3 (A)(4)(vi) "Aliens currently in deferred action status" are considered to be legally present in the country.

There is the whole argument of presence vs status, but most things really care about legal presence, not status. In order to get a drivers license you need legal presence. In order to be in the country legally you also need legal presence.