Submerged subs surfacing inshore are not a viable concern based on my knowledge and experience. Subs running on the surface are a threat as is any other M/V, for the same reasons.

Subs usually transit with escorts, who clear the inshore channels of all other traffic. The ports that subs normally transit into and out of are generally known and are allowed for by the locals. Subs do occasionally make Ports of Calls in unusual places such as New Orleans during the Mardi Gras, but these are again, to be expected. There are other non-sub based ports that see regular transits of subs, such as Groton, Cn and Cape Canaveral, Fl.

Boomers have air, sea, and subsurface escorts out from their portrs to the Continental shelf. Even someone who has no familiarization with submarine operations will take notice of that amount of activity. Someone will be along shortly if you're in a place that they don't want you in.