In the process of groping around in Safari's Preferences for a way to fix it, I realised that the otherwise indispensable Saft might actually be to blame. Sure enough, unchecking 'Always open browser window in a tab' in Saft's Tab pane did the trick. Obvious really. I think I originally checked it because I do otherwise like windows to open in tabs, but it's a bit over-eager, even though it does do exactly what it says on the tin.
Anyway, I'm now a happy bunny because bookmarklets open little popup windows as they were designed to do.