Thanks for you continuous effort on improving D Debian presence.
Could someone explain to me, for example, what should be the preferred way to package those? Should I package dub and make it build and install the files in some prefixed directory and just package that and copy it to a system wide directory (like /usr/include/d/ or something else)?
I think it is most simple an generic thing to do. Just run dub build on a source and then copy resulting binary and any extra files (man pages, modules, etc) to package. Exact placement in resulting file system does not have any common standard. For example, Jordi (maintainer of http://d-apt.sourceforge.net/) uses /usr/include/dmd as base for all imports and I have chosen common /usr/include/dlang/{dmd,ldc,gdc,whatever} for Arch Linux. I think you should actually have best judgement being Debian developer :)
dub does not have a make install alternative so it is completely up to package to chose exact file system placement.
Lot of dub packages are source libraries though (including vibe.d) - it is enough to just copy necessary module and define dependencies to get a usable package. Example of dub-free packaging I do for vibe.d in Arch : https://github.com/Dicebot/Arch-PKGBUILDs/blob/master/vibed/PKGBUILD (a bit outdated, oops!)
I'd love to read your opinion about desired scheme by the way ;)