To the point of the OP, I think it’s probably because mustard is generally more expensive and less frequently requested than ketchup. Packets of that kind of stuff in bulk are going to run about a penny each, plus the costs of stocking and transport etc., so call it 2 cents each. Then, if they are readily available, people will take them (thinking here of my grandmother, and her “if it’s not nailed down” theory of restaurant stockpiling). So it starts to add up. And believe me, these stores are making very thin margins to begin with, so your 99 cent value menu burger’s profit is probably wiped out by a few ketchup packets, let alone the more expensive “liquid gold” that is yellow mustard.
Since this is such a weighty issue, I thought I’d offer a clarification and a comment, and then I will tie all the plot lines together in a semi-amusing anecdote. Sort of like a mustard-themed Seinfeld.
Clarification to bradwalt: At McD’s, the mustard is not dolloped, as that implies a spoon or ladle being involved. In the world of McStandardization, this would leave too much room for individual discretion. Instead there is a doohickey that is basically an open metal pot with a trigger. When the trigger is pulled a set amount of the yellowest mustard you’ve ever seen is dropped onto the burger in a little star shape. More interesting is the caulk-gun-like contraption for “special sauce” which can shoot gook fifty feet or more.
Comment to RobV: Good show! Making fun of fast food employees is a challenging game, and you have shown both courage and wit in your mockery. In reality, though, some improbably large proportion of the population has worked in one of these places, including many of your SDMB peers. Many of the employees are short-timers, but among the other primary groups working at these places are the mentally handicapped, the elderly, and the poor. You showed them!
Climactic scene: Yours truly, circa 1990, dumps the entire mustard trigger-pot-thing into my lap in the first hour of an eight hour shift a la Polycarp’s story; acute cause was leaning on a counter to rest–thus violating the caridnal rule, “if you have time to lean you have time to clean”. Some smells and colors, it turns out, cannot even be removed from polyester uniform pants.