7 Wonders: Do board resources (brown and gray) count for VPs when counting guild and commerce points?
No.
The guilds in question specifically award points for cards.

Workers Guild: 1 victory point for each brown card present in the neighboring cities.
Shipowners Guild: 1 victory point for each brown, gray and purple card in your city. Clarification: the Shipowners Guild counts towards this total.
Craftmans Guild: 2 victory points for each gray card present in the neighboring cities.

And the last sentence in the base game Rulebook makes it clear this only refers to actual cards. [Emphasis added]

Clarification: Resources produced by boards are NOT considered as cards (Vineyard, Bazaar, Guilds, ...).