A decent size nuke is 200kt plus - if you look at nuclear torpedoes their yield is much less - thus if you want to sink ships and damage port facilities but not take out the whole port and city with it you would use a nuclear torpedo - but if you want to take out the port as a whole and sink as many ships as possible you use a much larger weapon
for instance the US Mark 45 torpedo only had an 11 kiloton warhead - still decent sized but hardly by itself big enough to take out a major port and the city surrounding it
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