The only reasons that I can think of are:
- someone drank or ate too close to when they collected the saliva, stripping their own DNA away before collection
- there's a mouth/throat/sinus candida or bacterial overgrowth that may be overwhelming the amount of actual human DNA in the saliva collection
As for other options; there are a few threads on this forum that discuss SNP analysis and different companies and what amount they analyse etc. There is also discussion about whether it's better to get WGS or WES. If the search function doesn't work too well via the forums, you can easily run a search of the forums via Google
From what I've gathered in other threads, while 23andMe used to be useful as a diagnostic starting point for PwME, 23andMe recently updated the SNPs it analyses. So it isn't as useful for us as a diagnostic tool as it used to be. (Apparently 23andMe is now focussing more on ancestry than diagnostics.)
It seems like Genos (WES) is one that Dr Ron Davis has been using as part of his research, and at around USD$400, it's more affordable than many others out there.
Dante Labs is an even newer kid on the block by many accounts, so it will be interesting to see how they deliver!