While what you say is true, it makes assumptions about the data. For example, maybe his data isn't continuous? Sometimes 0 isn't recorded and instead left as missing. If someone were to try and do a Oneway analysis using 0 as false and 1 as true they'd have a problem if their zero's ended up displaying as missing, since Oneway analysis ignores missing rows in JMP. They'd end up with ONLY ONE category!
There are other reasons 0 could show up as missing. Usually storing 0 in a large database is a waste of space. Since Pokemon Go is big right now, I'll use it as an example. I might want to record all the pokemon I caught in a day, 12 ratattas and 6 pidgeys. I wouldn't however, want to then store 0 for the other 148 pokemon I didn't catch that day. If I did I'd quickly fill up my database with useless information. Thus, if I queried my data I'd get missing for most of my pokemon at any given time, but missing is = to 0.
In similar situations you could get missing data that are equivalent to 0 b/c of data conversion issues, poorly designed queries, ect.