I tend to be of the view that all the heads can breathe fire rather than just one. Thus perhaps during the first round 2 decide to breath fire, during the second round another one breaths fire while the first two take a 1d4 round breather and the remaining heads consider breathing fire on the following rounds, etc.
Or, I suppose, you can limit the entire hydra to 1d4 rounds, but in that case all of the heads can (and should) breath fire the one round, then again all of them 1d4 rounds later. Otherwise, if only one head can breathe fire every 1d4 rounds, the ability is simply underpowered for the Hydra's CR. Hydras are meant to be a multi-creature, a serious menace that is difficult to slay.
One of the issues I have with D&D monsters is that many of them were unique - not merely rare - in the original mythology. These include the hydra, the chimera, the cerebus, etc. They were meant to represent major and unprecidented challenges to the various heroes of the myths, requiring from those heroes skill, luck, and insight, endurance, and combat ability well beyond what was typical.
This is not an issue readily dealt with in normal D&D games, I admit, unless one limits the appearance some creatures. Granted, all DMs do this to some degree anyway, if only limiting the ones they less like in favor of those they do like.