Vinyl flooring can be kind of brittle. Carefully assembling long seams together by hinging them into place should preserve the integrity of the long locking end, but I've seen a lot of short ends snap when hammered together (and there isn't a much better way to assemble them). It's a very big issue if hammered on when cold (where the flooring is both more brittle AND contracted), but not as much of an issue when the floor is warmed up to room temperature ahead of time.
So, if the short click ends to end up cracking, you don't have much of a choice to keep things together other than adhesive. That being said, I think I'd use a clear PVA like Weld-Bond before I used silicone. You want something that can flow into and fuse the crack, and maintain real structural integrity. Neither of those are something silicone excels at. A water based construction adhesive such as Loctite Power Grab would be an ok alternative.
