I suppose the fear is that the dogs will sniff out dope as well, and the casual toker will be put up against the wall and shot. I don’t think the transit police care about the average joint user, but it might also discourage using the subway as a distribution center for drugs. Boo. Hoo.
A jihadi planning to blow himself up will only be discouraged if he thinks he won't be able to take a bunch of Infidels with him. On the subway, or at a station, he's going to be able to do that as soon as the police start shooting, or at least he'll think he will be able to. Thus no deterrent effect from having the SWAT wanna bes in the subway system itself.
This being NY City, they won't be profiling riders for extra attention to those from groups more likely to be that jihadi, they'll be going after little old ladies of Russian Jewish ancestory and ethnic Chinese.