Multiple jets by RAW, but this likely wasn't intended
Compare the language in the multiheaded template from Savage Species. This template has pyro- and cryo- versions whose breath weapons use the exact same language as the hydra's, and are explicitly based on it:
Some multiheaded creatures have abilities similar to the various forms of hydras.
The template says that a multiheaded creature gets multiple jets:
Special Attacks: If the base creature has a breath weapon, the extra heads also have breath weapons. All weapons activate on the same round but can aim in differ-ent directions.
This template says the breath works like a hydra's, uses the same wording, and clearly says multiple heads result in multiple jets, which shows that this is the intended reading.
More detailed version: Suppose we read the hydra's ability to mean only one jet. Technically, in this case, a multiheaded creature with the pyro- or cryo- variant of the template would also only breathe once. That's because the "special attacks" quote above says "If the base creature has a breath weapon", and in this case the base creature doesn't have a breath weapon -- it only gains a breath weapon when the template is applied.
Thus, this reading creates a weird disjunction: a multiheaded creature who had a breath weapon before the template is applied would breathe multiple times, but a creature who gains a breath weapon from the template only breathes once.
That doesn't make sense, and the multiple jet reading resolves it. So we can conclude that the author of the multiheaded template understood the hydra's breath to have multiple jets.
Caveat: But how the writer of this template understood the hydra's breath weapon to work may not have been how the original writer of the hydra in the Monster Manual intended it to work, given the unclear language of the hydra's ability.
Conclusion: RAW, based on the text alone, hydras almost certainly breathe multiple times. But the original writer of the hydra probably intended one jet and worded it badly, because otherwise the damage is too high for its CR.
PS: Here are two homebrew ways you could change the hydra's breath weapon so the multi-jet reading is balanced:
- Use the multi-jet reading, make its breath line-shaped, and say the lines can't overlap (or that they don't deal cumulative damage when they do). A hydra has 16 adjacent spaces so this still creates a lot of variety. I think this is the most fun, and it reduces roll bloat because no one is making more than one save.
- Use the multi-jet reading but make each jet deal 1d6 per head, not 3d6.