The term base-deactivated silica means absolutely nothing, with the exception that the company that is trying to sell you such a thing wants to tell you that such packings are suitable for the chromatography of bases - whatever that means...
A better and more meaning nomenclature is to differentiate silicas into high-purity silicas, commonly made from a tetraalkoxysilane, combined with using metal-free reagents and reaction vessels, and low-purity silicas, made from inorganic precursors such as water glass or similar that contain a more-or-less high level of other metal oxides, such as aluminum or iron oxide. The high-purity silicas became for the most part first available in the early 1990s, although materials of a reasonable quality existed already in the 1980s.
When you have a contamination of iron or aluminum in the matrix of the silica, this creates acidic silanol groups on the surface of the silica, and these acidic silanols are bad for basic analytes, i.e. create tailing. With a well prepared high-purity silica, this problem does not exist. Note that there is no way to turn a low purity silica into a high-purity silica, since the contamination is in the matrix.
Due to the fact that these older silica give tailing peaks for bases, there was in the late 1980s to early 1990s a trend to endcap these packings with an amino silane. When you do that, you can eliminate the tailing of basic analytes, but now you can't get acidic analytes off the column any more. Anyway, this may be the place where the name "base-deactivated silica" is coming from. However, today the meaning is rather fuzzy, and I suspect that many silicas are base deactivated by showing a bottle of base to the silica before starting the bonding reaction. Then the silica knows that it has been "base-deactivated" and will act accordingly.