I am... dubious of the actual danger EMP poses to submarines. If they were surfaced, especially if they were attempting to recieve radio communications, sure. But a submerged submarine would be extremely well shielded.
The real question would be whether a submarine captain would be willing to press the button based on radio silence alone.
From the report linked, on the threat to communications between submarines and command, and the direct threat to submarines:
>> HEMP Threat To U.S. Submarines?
> HEMP attack could achieve for Russia a key objective the USSR could not achieve during the Cold War—neutralizing U.S. ballistic missile submarines at sea.
> Russian Super-EMP weapons could destroy or degrade U.S. bombers, ICBMs, SSBNs in port and their strategic C3I—including land-based VLF communications systems, TACAMO aircraft, and other redundant means of strategic command and control used to convey Emergency Action Messages (EAMs) to submarines hiding at sea. Severing their communications links to the National Command Authority would neutralize U.S. submarines, rendering them useless.
> HEMP could also be used to attack submarines on patrol at sea directly.
> A high-yield warhead (1 megaton or more) detonated for HEMP over the ocean would cover an area 2,200 kilometers in radius, a zone nearly as large as North America, with powerful E3 HEMP that would penetrate the ocean depths and possibly damage or destroy the electronics of submarines on patrol. Submarines would be especially vulnerable when deploying their very long antennae—which they need to do precisely when trying to receive EAMS.
The real question would be whether a submarine captain would be willing to press the button based on radio silence alone.