Of course the 'tech tree' in MOM is a bit shallow.
There was no 'tech' tree in MoM. There was simply a magic tree for unlocking new spells but that was it. Everything other then spells you started the game with access to you just had to build it and it's requirements first. MoM had more of an RTS feel with buildings and unit production.
In fact the focus on the Magic tree was often the thing that allowed people to do huge exploits in MoM. You could start the game with some of the best spells in the game if you got enough books in that area. Sure you couldn't cast them very quickly but just 1-2 of the most powerful summoned monsters in any line could sweep the starting map with little to no effort.
While the counter route of non-magically could rarely do anything to stop it even against AI on impossible difficulty which had like a 50% bonus to all production as I recall if not more. They'd have whole armies of units while you'd have just a few and the uber summon units were often the only counter. On normal difficulty it wasn't even a challenge really.
I'd say that the lack of a tech system is really what made the "military" pick like warlord so valuable. You either went with units that could gain XP or you didn't. If you went the route with units that earned XP then letting them level up higher really helped. While if you went the summon unit route it was a rather worthless pick. So it depended more on what units you plan to use rather then a military vs tech choice.
As for the original topic I think part of the reason that war bonuses get over shadowed by tech is due to imbalancing in how fast tech power grows compared to the war bonus. Some games give a static bonus and while it makes the problem worst a percentage bonus also often doesn't measure up.
The reason is say at tech level 1 units has 1 strength, Tech 2 is 2 strength, Tech 3 is 4 strength and so on. This basic doubling effect while not exact is kind of the model games like Civ and Gal Civ follow where the next weapon/unit/tech continue to have even greater bonus then the one before it especially at the end of the tech tree. Take Civ4 for example when you got from Musketers at STR9, to Rifleman at STR14, to Mechanized Inf at STR 32. Now a 10, 20, or even 30% bonus isn't going to offset that tech jump.
Usually a tech focused side can keep 1 or more tech levels above a war race. Even if you get a war based race the benefit of increased tech stealing when capturing cities/planets like some suggestion. The problem is the war race can never effectively over take any race because they are totally dependent on other races to have developed it first just like the spy focused race. Thus they will always be behind or equal to the tech race. They can only over take them after having destroyed enough of their production base that the tech race can't R&D faster then them, such as the war like race has 20% more income put into R&D then the tech race who gets a 20% bonus to R&D. Then they end up researching at the same rate, meaning the war empire needs to be about 20% larger most likely. If the tech race has a larger empire though then the war like one's only real hope is to rush them and undermine their production enough to over take them on R&D.
Personally I do think the R&D bonus to military field is the better approach. Though it does still pose the problem of late game usefulness. At least with the bonus to combat itself there is a slight advantage when players are on equal tech terms, such as late game when they both have reached tech limit. What it comes down to more often is a balance issue.
Though in closing I've never really liked how most 4x games handle war like races. They tend to give them simple bonuses to combat and that's it. They still suffer penalties with war and unhappiness that other races do, though in some cases it's slightly less, which in my opinion doesn't make any sense. Someone already mentioned the Klingons so I'll use them again as an example. The Klingons love war and would not become unhappy that were at war unless maybe they were losing it badly but even then it would spur them onward even more. Even in human history curtain nations loved warfare and were always at war with someone yet their people thrived and encouraged it. They didn't rebel and become unhappy like a bunch of anti-war pacifist we have today.
Some cultures find nothing wrong with war as a way of life and wouldn't suffer any penalties from it. Even peaceful nations who don't like war tend to toughen up when they are in a defensive war against an outside aggressor. Though as far as I can tell E:WoM doesn't have any kind of war wariness mechanic so this shouldn't be an issue.