Recharge X-Y. The notation “Recharge X-Y” means a monster can use a special ability once and that the ability then has a random chance of recharging during each subsequent round of combat. At the start of each of the monster’s turns, roll a d6. If the roll is one of the numbers in the recharge notation, the monster regains the use of the special ability. The ability also recharges when the monster finishes a short or long rest.
This notation is attached to an individual ability. It indicates that the ability it is attached to has, as additional rules beyond its individual description, these rules as well. You could replace the “Recharge X–Y” notation with these rules to achieve the same effect; the notation just saves space and is easier to remember.
Considering that, then, let’s consider the one monster that appears to actually have multiple recharge abilities:
Lightning Strike. The giant hurls a magical lightning bolt at a point it can see within 500 feet of it. Each creature within 10 feet of that point must make a DC 17 Dexterity saving throw, taking 54 (12d8) lightning damage on a failed save, or half as much damage on a successful one. [The giant can use Lightning Strike once and it then has a random chance of recharging during each subsequent round of combat. At the start of each of the giant’s turns, roll a d6. If the roll is a 5 or 6, the giant regains the use of Lightning Strike. Lightning Strike also recharges when the giant finishes a short or long rest.]
Thunderous Stomp. The storm giant stomps the ground, triggering a thunderclap. All other creatures within 15 feet of the giant must succeed on a DC 17 Constitution saving throw or take 33 (6d10) thunder damage and be deafened until the start of the giant’s next turn. On a successful save, a creature takes half as much damage and isn’t deafened. The thunderclap can be heard out to a range of 1,200 feet. [The giant can use Thunderous Stomp once and it then has a random chance of recharging during each subsequent round of combat. At the start of each of the giant’s turns, roll a d6. If the roll is a 6, the giant regains the use of Thunderous Stomp. Thunderous Stomp also recharges when the giant finishes a short or long rest.]
Written out this way, it’s clear that it’s a separate d6 roll for each ability if both are discharged. The wording of the “Recharge X–Y” notation description is consistent with this: it says “the roll” allows the monster to regain “the use of the special ability.” That is, one roll, one special ability. If there are multiple special abilities, they get multiple rolls. The rules do not allow for a single roll to govern the recharge of more than one ability through this notation (a situation like that would likely have to be spelled out in more detail rather than rely on the “Recharge X–Y” notation—see dragons’ breath weapons for a possible example of a somewhat-similar situation).
However, in a publication... you might want a reminder
Note that, per the various answers to this question, this isn’t clear to a lot of folks. The text certainly doesn’t explicitly cover the situation, as the fact you needed to ask the question might itself indicate. And the variant Storm Giant seems to be literally the only official monster that includes more than one of these abilities, which means that, ultimately, the rules text might not be explicit here because they didn’t think it would ever come up—monsters would generally have at most one such ability.
So if you plan on having multiple recharge abilities on your monsters, and you want other DMs to understand what you mean, you might include a sidebar on the subject explaining exactly what you mean. Wizards of the Coast probably ought to have done so when they first introduced a creature with multiple recharge abilities, but they did not. I would.
(If you’re just homebrewing monsters for your own campaign, of course, this is less important.)