Yes, losing a percent modifier to your overall production is a huge detriment. 1 extra hammer per forest rarely if ever makes up for it. Percent modifiers which build off your total hammers are extremely strong late in the game when you have 80 - 100+ hammers.
Depending on the situation, the Longhouse could still actually be better in production, and even more so when stacked with other percentage bonuses to production, such as railroads, factories or golden ages. Also, it goes without saying, the more forest tiles, the better.
Say for example, if there's a city with 3 forest tiles and 25 more production from other sources, turning all of them into lumber mills will yield a total of 34.1 production, which already includes the workshop bonus. A longhouse instead would yield 34 production, barely only losing to the workshop. However, when adding the 20% bonus from golden ages, the workshop provides only 40.3 production, while the longhouse provides 40.8 production, which surprisingly makes it better, if slightly.
There is a catch, though. It only works if you compare it with cities with lumber mills. If all three forest tiles could be converted into hill mines, then the workshop is obviously better in terms of production. Suddenly, the workshop provides 37.4 production and 44.2 production with the golden age, a far cry from the longhouse. Let's not even go to the Order tenets.
However, again, it also loses three food, meaning suddenly, the longhouse is better in another aspect. If the city has a population of 10, gaining 5 excess food (not accounting the forests/mines), has no aqueducts yet, and is growing on standard speed (growth rate is 0/114), it means the workshop city replacing the forest tiles with mines will grow in 23 turns, whereas the longhouse provides 3 additional food (excess of 8 food) from forest tiles thus will grow in only 15 turns. The situation is suddenly comparable to the Incas where they can forego production in exchange for more food generated by terrace farms.
The underlying problem now becomes this. It's not because the longhouse loses its 10% bonus that makes it bad. It's because the longhouse forces the Iroquois to settle on areas with forests, preferrably a lot of them. I have a Petra city in my current game which, while makes it great in terms of production and food and even has access to 5 forest tiles, is still flat out worse if compared to the same city built by another civ. The longhouse has no redeeming qualities when it comes to land that isn't dominated by forest tiles, and this specialization is what makes it crippling to the Iroquois. At least the Incas have no problems working on flatlands as they can be played out like any other civs. The Iroquois, not so much.