Well, technically, Topaz *is* a newer format designed to (among other things) make decrypting harder. So you're right about that.
Amazon had bought .mobi when they purchased the Mobipocket operation outright, and went and commissioned a new format for a variety of reasons and it was years before anyone went and reverse-engineered it. Here's a
blog entry with comments by one of the programmers who helped created it.
However, it's mostly been used for older books because it started as a quick and easy way for publishers to get their books on Kindle cheaply so that Amazon could have a larger catalogue to supply its users. Nowadays many publishers have made ebook releases part of their production flow, and sell in more than one store.
Amazon now provides tools to convert ePub files to Mobipocket format for submission, so it's probably more cost effective for the publishers to come up with an ePub file that they can then send practically everywhere after a little tweaking to make it fit the various store requirements, instead of both commissioning an ePub and also paying Amazon to convert a Topaz for them.
That's likely why, to give an example, you may get an older series that starts off Topaz, but the newest books in it are Mobi, like the Billy Boyle series where the first book was a freebie a couple of months back at both Amazon and B&N.
Here's the 5th book, released in August this year:
both a Print Length and a File Size, so Mobipocket.
But up to the 3rd book, released in 2008 when the Kindle was just coming out, it's
Print Length only.
Back then, the Nook and other competitors simply didn't exist, ePub probably was a blip on the radar of most folks, and Soho Press seems to be one of the smaller imprints.
Having their book sold by Amazon for its trendy new device getting press coverage, instead of one of the less well-known-to-the-general-public stores like Fictionwise, probably seemed like a better idea than releasing it who-knew-where-in-whatever-format to sell in unguessable quantities. And Amazon would even make the ebooks for them, too!
But then the B&N, Sony Reader, and Kobo stores came along, so if they wanted to have the entire series available for those readers, they now also had to pony up an ePub for the earlier books, which is why I ended up converting the B&N freebie to read on my Kindle instead.
I strongly suspect this is the situation behind many of the Topaz books available in ePub at other stores nowadays, and most publishers just doesn't want to go through the trouble of converting and resubmitting a Mobi version even if they have the means to do so, now that they're selling elsewhere as well as Amazon.