Even if the older Route packs work with TRS 2009, and I guess they eventually will, any routes you're currently using will still display the the older style assets currently associated with TRS 2006. In other words, TRS 2009 won't be able to turn your favourite signal box into a super high resolution building. The signal box will still look the same as it did in TRS 2006.
Eventually, the content creators will replace many of the older assets with new ones that "will" look better in TRS 2009, but that will all take time.
The TRS 2009 developers are well aware that assets currently on the downlaod station have taken Trainz devotees over 500 man years to create. The last thing they want to do is dump all that hard work into the garbage bin, so they'll do everything in their power to get existing assets to work with TRS 2009. I'm sure this will include the routes, but these may need to be modified by the creator and reinstalled by your good self before they will work properly.
Once again, any assets used on that route will continue to be TRS 2006 low poly/low res assets unless the route designer can find similar TRS 2009 high res assets to replace them with.
It's early days, so the only thing we can be certain about at this point of time is death and taxes!