In a torrid affair, spoiled by a gale-force wind, Pools failed to score a goal for the sixth game in succession.
Hughes' side dropped bottom of League One after a third successive 0-0 draw at Victoria Park.
Hughes, whose side had the game's best opening when Antony Sweeney was denied by Johnstone, said: "In terms of effort and shape it was positive. We didn't capitalise like the other night.
"I've seen us play better, a lot better. That's the disappointment.
"We showed spirit and battled hard. Now we need a system to score goals and win games - even if we go gung-ho then we will have to.
"You have to praise the two defences, we edged the first-half, second half was more Walsall. We are thankful some players left their shooting boots at home and they fired over the bar.
"We are up against a team going for the play-offs, we are at the bottom.
"I want to drive this club forward and implement a style of football that people can be proud of and we are a few years away from it.
"But we have put pride back in the club and we are getting there."