I have two cofounders who I've worked with in a similar capacity. Can they write a joint letter of recommendation for me?
That would be up to the receiving institution to judge, but I suspect so. But it would possibly count as one letter of the (likely) three that you need, however.
Individual letters might be a bit better, though, as it is clearer where the ideas in it come from. And given that you have a continuing relationship with them, there might arise questions of conflict of interest.
Note also, that for graduate (especially doctoral) admissions, the writer needs to be in a position to know what is entailed and to make an honest prediction of your likely success. "Two cofounders" might be in a position to know that, or not.
Yes, they certainly can. My lab head and I have done this for students I have directly supervised so that they have the benefit of my detailed comments on their day-to-day performance, and also the name recognition that comes with my supervisor's name on the letter.
In situations like this, it is common for one of the authors to write the letter, give the other an opportunity to look it over and give additional comments/approval, and then that author will submit the joint letter to the institution.
This generally only counts as one letter of recommendation.
Why aren't both of them writing letters? Typically, recommendation letters aim to provide a 'personal' perspective from a supervisor, co-author, director, etc. Since both of them may not be able to assess your qualities in the exact same manner, I don't think it's a good idea.
Another consideration is that each person writing a recommendation letter usually starts by explaining how and in what circumstances they worked with you. I assume that you interacted with these two individuals in different situations, and they likely had distinct experiences with you. Even if the experiences are somewhat similar, there are likely differences.
To illustrate, suppose person A is experienced in task A1, while person B is experienced in task B1. Even if you performed well in both tasks, they would (and should) likely focus their feedback on their respective areas of expertise.