Hmm, that's odd. I even see a single store (Queen Creek Bricks, the cheapest source of the plain helm in large quantity) that sells the plain helm for fifty cents more than the printed one. Your explanation is the only one that I can see. I could see that some people might want to have a small number of printed helms for officers and a larger number of plain ones for regular solders, but quite frankly I'd rather just have printed ones. It's not like the 'Eomer' helm is obviously set apart, like only wanting one Darth Vader but an army of Stormtroopers, or just one crown and a bunch of normal helms, etc. Heck, I think it would be fine to mix a bunch of Theoden helms into an army, if you're not completely set on following LEGO's direction on this.
Ooh, maybe this is the answer: Perhaps it is the Eomer fig as a whole that people only want one of, while they want a lot of the general soldier. And so people are buying up more of the general Rohirrim soldier as a whole unit, while more of the leftover Eomers are getting broken up into parts, driving down the prices of the various Eomer parts? As evidence, I note that in the Bricklink price guide, just taking the used fig average price for the last six months, Eomer goes for 5.35, while the soldier goes for 6.93. Also the soldier's torso is on average thirty cents more expensive than Eomer's.
IMO it would be perfectly fine to mix a bunch of Eomer torsos into a a general Rohirrim army. I don't imagine that an army such as that would be completely uniform (perhaps with an exception for the king's elite guard), so if I were trying to make a large Rohirrim army I'd mix it up. I'd put in both the Eomer and soldier torsos, swap around the arm colors to get some variation, throw in a few other castle torsos of similar color scheme, and vary up the helms a bit (use both of the official Rohan helms, maybe another helm that doesn't clash too much, give a few of the guys here or there a hood or just hair). Randomly give some figs capes of relevant colors. Change up the weaponry a bit - use different spears and bows, for instance. Give some shields and others not. I'd probably leave Theoden as the official fig to keep him distinct, and maybe to make Eomer stand out I'd have him without a helm - I think he's described as having long blonde hair, though I don't have the book here and I might be letting the PJ movies and/or various fan art influence my recollection here. I tend to give my 'hero' figs the big old-school chrome greatsword. I know it's a little cartoonishly large, but it makes them stand out.