Changing the default due time doesn't change the due time on actions/projects that are already in your database.
And your 2nd paragraph raises one of the central questions of GTD. OmniFocus's tools for shortening that list of hundreds of actions include the following:
1. Contexts--select the contexts available to you, or where you want to be.
2. Focus--focus on the project(s) you want to move forward, so you're not distracted by others. If you organize your projects and single-action lists into folders corresponding to areas of responsibiity, you can cut out a lot of clutter by focusing on one or two folders. I find this immensely helpful in avoiding procrastination.
3. Available time--if you systematically enter estimated duration (and you're honest with your estimates), you can shorten the list by filtering on duration--short durations if you don't have much time or want to get a bunch of short actions checked off; >1 hour if you have a big block of time and want to make the most of it.
4. Start dates--use them to defer actions or projects that are, for the moment, lower priority. (You can always change them back during your daily or weekly review.)
5. Flags--I like to use flags for those projects or actions that are not due any time soon but that are important to keep working on regularly in order to make progress and not be caught by surprise. Others clear their flags daily and then use flags to mark the top things to do today. Others use flags to mark things they want to be reminded of on their iPhone.
Ken Case wrote
a good post not too long ago about how to use OF to shorten that daunting list. Many of his ideas are similar (not surprising: he's running the show, and I've been using OmniFocus for 14 months and have watched many of its features develop).