Yeah, those whips are often to give them some level of performance around the 6 meter band. They are not great performers there, and the ground plane provided by the discone reduces the performance even more. If you have no interest in those lower bands, it is absolutely OK to remove it.
You don't want the socket to fill with rain water, so it's a good idea to plug it. You'll probably find it uses the standard 3/8" x 24 threads per inch antenna mount sized used by many CB antennas. Go to a hardware store and get a stainless 3/8x24 bolt that will thread in there. Maybe seal it up with some silicone for good measure.
Pretty sure I did that with my Diamond D130 discone.
