Is there any linguistic reason for the words tough, though, plough, and thorough having such different endings?

The answer is not great:

Middle English phonology – Wikipedia

The phoneme /h/, when it occurred in the syllable coda, is believed to have had two allophones: the voiceless palatal fricative [ç], occurring after front vowels, and the voiceless velar fricative [x], occurring after back vowels. The usual spelling in both cases was ⟨gh⟩, which is retained today in words like night and taught.

These sounds were lost during the later Middle English and Early Modern English eras. The timing of this process was dependent on dialect; the fricatives were still pronounced in some educated speech in the 16th century, but they had disappeared by the late 17th. Loss of the fricatives was accompanied by some compensatory lengthening or diphthongization of preceding vowels. In some cases, the velar fricative [x] developed into /f/; as such the preceding vowel was shortened, and the [u] of a diphthong was absorbed. However, the palatal fricative [ç] in no instances became /f/.

Some possible developments are illustrated below:

  • OE niht (‘night’) > ME /niht/ [niçt] > /niːt/ > NE /naɪt/ (by the Great Vowel Shift)
  • OE hlæhhan (‘to laugh’) > ME [lauxə] > LLME /laf/ > ENE /laːf/ > NE /læ(ː)f, lɑːf/
  • OE tōh (‘tough’) > ME [tuːx] > LLME /tuf/ > NE /tʌf/

This variable outcome, along with other variable changes and the ambiguity of the Middle English spelling <ou> (either /ou/ or /uː/ in Early Middle English) accounts for the numerous pronunciations of Modern English words in -ough- (e.g. though, through, bough, rough, trough, thought, with -ough- pronounced /ou/, /uː/, /au/, /ʌf/, /ɒf/, /ɔː/ respectively).

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