You know, I think it is unfair. Why Mac App Store users get updates for free and we just bought the app in your store have to pay again?
All website customers who bought 1Password 3 in the last 9 months (the year 2013) from our website will get a free upgrade to 1Password 4. A lot of 1Password 3 website customers paid the upgrade fee to get the MAS version even though the MAS version was still at 3.x. That's why it is free for everybody who bought at the Mac App Store.
So if you've "just bought" 1Password 3 from our website this year you're certainly eligible for its free 1Password 4 upgrade. Qualifying customers will be receiving email about this soon.
Is this upgrade model expected to be reused for 1Password 5? i.e. is the 'free upgrade' for MAS users the norm, or just something you decided to do this time for some specific reason?
No, 1Password 5 will not likely follow this path. As @Sjk mentioned, we did this because 1Password 3 at the Mac App Store was released while the website version was also at version 3. So, many folks paid to convert to the Mac App Store, even though they own the same version. Since 1Password 4 are released at the same time for both Mac App Store and our website, it'll be different next time for 1Password 5.
However, since it's been 4 years between 1Password 3 and 1Password 4, we can't really predict what'll happen in a few years. Who knows, Apple might actually change their mind and provide the ability to offer upgrade pricing.