Considering most MOS users I know have at least 2 or more registrations that's hopefully close to 1000 users.
That sounds reasonable IMHO. Some users of course have only one MorphOS system registered, while others may have a couple, but an
average of 2 copies per user does indeed sound like a fair guesstimate.
A few years ago, most people would guess around 700 users, but a lot has been happening to both MorphOS's features and the supported HW platforms since then that without doubt has made the package more attractive. So about 1000 (more or less active) users, or perhaps "unique license owners" would be more appropriate in this context, seems indeed very realistic.
I honestly thought there'd be alot more.
Then I think your expectations about the interest in "Alternative" OS's in general and Amiga related OS's in particular in 2013 is very unrealistic, especially since it's only running on PPC machines with 2005 (tops) level performance. It's obviously only the surviving but steadily diminishing Amiga community that cares. When (if) it would get to run on modern HW like x86, then the situation
may become different. Until it does, this is very good numbers IMHO.
This is a lot better than I personally dared to hope for!
So much for the 'cheap hardware will bring the masses' crowd. It appears there's a lot more than cheap entry into ones decision in choosing an alternative OS.
The diversity of available HW platforms (both tiny footprint, big box and laptops) has only been good for MorphOS, the statistics clearly shows that if you look at how the graph develops during a month after support for a new platform has been introduced. In several occasions it has also made the graph
steeper (an increase in the
growth rate, that has then lasted). In retrospect, the decision to support second hand, mainstream PPC Mac HW was a
brilliant move. The low cost, the diversity and the performance (the Mac PPC HW represents the peak of PPC, it's as far as the PPC ever went on desktops/laptops) has definitely paid off!
These license numbers could not have been reached without the Mac HW support. It surely made MorphOS a lot more available to Amiga enthusiasts. Which for obvious reasons are the only ones interested in MorphOS, not "the masses" as you seem to believe. It's all a zero sum game within the ever-shrinking Amiga (NG) community. And for sure these high numbers could *never* have happened if the MorphOS team had put their hope to €1,000 Sam 460 systems or $3,000+ X1000 systems.