Why not exactly? The only thing you really have to do for an endorsement deal is use the equipment and put a little note in your CD booklet or something. That's it. If you can get a few hundred or free equipment for doing basically nothing at all then how on earth is that not worth your while? Most artists only get endorsement deals for equipment they were already using in the first place so it's basically free money/gear. And loads of bands have endorsements for various brands, you don't seriously think that every underground metal drummer that endorses "brand X" cymbals is going to get $5,000 for that.
The equipment manufacturers look at it purely from a marketing point of view. Is the fact that band X endorses our product Y going to result in additional purchases for that product? For most underground metal bands it will be next to irrelevant (at best it might give the brand some underground credibility if they manage to amass a decent amount of endorsements from respected underground bands) and they are obviously not going to shell out large amounts of money for those.
And your royalties story is nice and all, but you do realize you need to sell a fuckload of records for that to really mean anything. Opeth sold like 80,000 copies of BWP and that was at a time when they were still barely able to live off of their music. The majority of underground bands don't get even close to those figures in terms of sales. And if you are an underground band you are not really in any position to demand anything from record labels in terms of royalty percentages. Both because you yourself are barely commercially viable and because the only labels that are interested in you will be relatively small/poor themselves. Until you break out of that (like Opeth did when they became more popular and signed to a big label like Roadrunner) you are pretty much stuck with whatever deal you can get.