Yes, when scoring Link tiles at the end of an era, you score 1 VP for each industry icon in adjacent locations, regardless of whether the adjacent tiles are flipped or unflipped.

This is supported by the following rule:

• "For each of your Link tiles, score 1 VP for each [industry icon] displayed in adjacent locations, by advancing your VP Marker along the Progress Track. Remove Link tiles from the board as they are scored."
  (Page 7)

The rule does not specify that the industry tiles must be flipped; it only refers to the presence of the industry icon in adjacent locations.

Source: page 7.

Source: Core Rulebook (pp. 12, 5, 6, 7, 8)