The thing is this: when producing music on a computer, you're going through different processes.
Scoring, or writing, is one thing. Some people feel more comfortable scoring "traditionally" in a software like Sibelius. Others have adopted methods and proficiency in writing directly "into the DAW", either by playing all the parts in with a MIDI keyboard, or by clicking in the notes into the piano roll editor.
It doesn't really matter. Both methods are just there to provide the sampler the information about what notes and instruments are to be made to sound where and when.
The real point is that when you're doing music on a computer, working with samples, etc., what you're essentially doing is music production - make no mistake. It's OK if you're using samples and a notation program to formulate a composition and produce an audible reference. But if the end result is supposed to be something "listenable", with musical qualities, something that's supposed to be usable perhaps in a media context or even trick the lay person into believing that they're hearing a real recording - then I don't see how you could bypass the processes of digital music production, and thus, the DAW.
Samples won't sound musical on their own, without any "massaging" in a good MIDI editor. That's an art in itself. This is where all the intended nuances of musical delivery, articulation and phrasing, dynamics etc. are worked in. For example, this is where you would deliberately move and displace notes around the grids of the musical meter to create plausible effects of agogics, rubato etc. Note lengths and envelopes are manipulated to make note durations, accents and releases musical sounding. This is of vital importance especially for runs, ostinati, agile phrases that switch between detaché and slurred playing, etc. Dynamic curves are applied to notes to manipulate the musical expression and to tell the "player" exactly how and when to suddenly become louder, or softer, to advance or fall back, to suppress the motion or to explode.
If we decide to embark on this somewhat bizzare quest of trying to make computers, loaded with pre-recorded, isolated samples of instruments, produce something that somewhat resembles real music, than the MIDI programming makes a world of difference. It's just a whole different process and an art in itself, that comes AFTER the process of writing and notating the music. Let's put it this way: notating in Sibelius or Finale tells the sampler what instrument should play which notes, when and where and by using which technique. The MIDI programming in the DAW tells the sampler everything about the musical delivery, the "interpretation" and the feel of the music. Both processes are equally important.
And then there's the whole other topic - and the next in the series of related work processes - of mixing the music, i.e., making it sound good and pleasing on an audio level. This is another area where an already well written and skillfully programmed piece can be made to shine and come to life even more.
Long story made short: working in a DAW makes sense because it's just a better-suited and more advanced environment for MIDI programming and music production tasks. You may be able to do some of it in a notation program, but that's not what those programs are made for and for "serious" results, I would really really recommend importing the finished score as MIDI into a DAW and take it further from there. One just has to view it as separate processes, and choose the appropriate tools for them.
Most people I know who like to compose in standard notation first and deal with sample programming later, work in dedicated notation software like Sibelius and Finale. The included notation capabilities of DAWs like Cubase or Logic just aren't on par yet. There is however talks of Steinberg developing something new in the notation department and integrating it into Cubase - if I understand correctly, they actually employed the team that developed Sibelius. So perhaps there may be finally something coming up that has the potential to unify the processes of notation, programming and audio production in one package on an overall satisfying level.
