I'm not sure exactly how you come up with 28 consonants in English. The rule you refer to applies to any letter that is *pronounced* as a consonant, including the "w" (although I can't think of any nouns or verbs ending in "-wy" off hand). Obviously, no word in English ends in a double "y."
The true version of the rule is that whenever final "y" is the main vowel in its syllable (ie the "nucleus"), we change the spelling to "ie" before adding "s." This is a spelling change only -- it has no effect on pronunciation. If on the other hand, the "y" is merely a semi-vowel, ie, preceded by a main vowel as syllable nucleus, the "y" remains and only an "s" is added.
sixty / sixties, doggy / doggies, study / studies, fly / flies
day / days, pay /pays, key / keys
special case: money / monies