Yes, for city-based "Highlight of the Day" bonuses, Walk cards—whether left face-down or activated face-up—are counted as being in the city indicated on the back of the card.

This is supported by the following rule:

• "Remember that for any card with a yellow background, a player chooses whether to count it as Tokyo or Kyoto. However, Walk cards, whether left face-down or activated face-up, are counted as being in the city indicated on the back of the card."
  (page 15)

Therefore, even if a Walk card is later revealed to have a yellow background when played face-up, it still counts as being in the city shown on its back for the purposes of city-based bonuses.

Source: page 15.

Source: Base Rules (pp. 10, 15, 6, 7, 8)