I can only speak for Premiere Pro 2.0, but I assume that other pro NLEs have similar options -
It is too time consuming to mark in and out points, in the camera. I use "auto pilot" to capture my clips. When my project is complete, if I want to archive it, PP has a way to save just the used materials into another folder. I can archive this folder, (with only the clips I've actually used) and then delete the original folder with all the captured clips and other files.
I have over a terrabyte of harddrive space, including three internal drives and several external drives. I can quickly remove an external drive and insert a new drive in the case, for accessing archived projects. All drives are SATA.
When I first got back into video, several years ago, we used to review tapes in their entirety and either manually select live capture or mark in and out points. It took just one time for my NLE to "forget" the in/out marks that it took us hours to select, to make me swear off this time-consuming practice. I've never looked back. You have to review everything at one time or another, why not just do it all at one time - during editing?