Everyone, thanks for the input. Many excellent ideas there.
Here follows a report of how I managed the hydra, and how my players enjoyed it.
As an introduction, I looked at how RMU manages it. Well, not so well either… Though it's better in that, by default, one always hits a head, so the body may only be hit through a called shot, there's no ruling about
how to determine that a head is "killed" or severed, nor how to stop it growing back into two heads. There's no "primary head" BTW.
Anyway, rdanhenry's initial idea of treating each head, the primary head and the body as independent opponents, furthered by Jengada's detailed answer was my starting point. I considered the primary head and body as a H/SL 380G AT19(40) creature without the breath attack, and gave each head 10% of the hit points, rounded up, so each was a H/LA 40G AT19(40) creature with a breath attack.
As I really think a head should be severed to "defeat", I ruled that a head only takes one third damage from any attack (including magical) not associated with a slash critical, with the body and primary head taking full damage. Once a head reaches 0 hit points, it is considered "severed" and starts to regenerate (in 2d10 rounds); whilst it's doing so, any heat critical cauterises it. For tries made from torch attacks, I "merely" used the "attack with torch" rules from the "
Arms Companion" (chapter 6.27, p48). Oh, and it may not have more than ten heads in all at a given time. :p
I didn't use Elrich Maltah's suggestion about the A.C.'s strategic targeting rules, because I would have needed to create and assign the B.A.M. and random hit location table, since these rules are pretty much just the (old) RuneQuest location rules adapted to RM2… and a pain to do all by oneself.
All in all, my players loved it… meaning that they found the hydra to be a pain in the ass. Considering their experience as players, meaning they all knew what an hydra is and how it's supposed to be defeated, and the fact the characters were prepared, the hydra being able to go beyond their expectations, be a pain, and provide an interesting combat gaming experience is what I consider a success.
So, many thanks to all of you guys!
P.S. If any RMU's team member is reading this, he may want to go back and redesign the hydra in RMU.