I second MetzFan's caution about storing in plastic, and will share my experience of having bought pre-loved scarves which had been stored in zip-lock bags. I had to steam AND freeze them multiple times to get all the odor out. The first couple of passes with the steamer smelled like I was cooking some nightmarish vegetable medley (I hate cauliflower). Obviously, something had been growing.
Sources: if you can't access a website with archival materials, I would call a local museum which has a textiles department and ask them for a source for archival materials.
Yes, the Hermes liner papers are acid free (and contain silk, I was recently told, which explains the fragrance I swore I'd been detecting).
My smallish collection is stored in a wide though rather deep dresser drawer. I have the boxes open, lids underneath, four across, and stacked four or five high and staggered front to back. Some boxes have a second scarf folded in half and laid atop the first. Now...where the sweaters in the drawer below will move when they get evicted in favor of more scarves is, as yet, undetermined.

The scarves are loosely stacked according to color. I keep my one silk jersey in a closed box, and my two GMs separately in closed boxes, as well.
I, too, keep the store tag, tucking it beneath the tissue paper in the box. I also usually remove the care tags, and keep those there, as well. Like others, I keep an Excel spreadsheet of my collection, with name, issue, acquisition date (and giver, if a gift), location, reeference & colorway number and color names, and cells with the primary, secondary, and tertiary colors of the scarves filled in, to help with shopping.