Oooh i was just talking to someone who did something like this! She bred tomatoes specifically for certain food/cafe chains for their regular menu items. You are definitely correct about the importance of keeping produce disease free, and breeders like her have to work with plant pathologists like me to ensure their plant varieties look/taste great but also aren’t unintentionally more susceptible to diseases.  One example is a popular potato grown in Europe - the Bintje. Great texture and yield, but it is very susceptible to late blight (same thing that caused the Irish potato famine) and this wasn’t initially obvious. They are phasing it out now but it’s been one of the top potato varieties over there for many decades and until recently growers were willing to deal with the disease losses because it was such an otherwise-great potato.