I can pronounce it both ways below:
I think #2 is the correct way but when I listen to this word's pronunciation on Google Translate, which you can slow down, it sounds like #1.
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Correct me if I'm wrong, but I don't think the Korean sound system has a meaningful distinction between "깨끋타다" and "깨끄타다". In other words, there is not a meaningful difference between /V1 ㅌ V2/ vs. /V1 ㄷ ㅌ V2/, where V1 and V2 are some vowels.
So it's a bit like asking whether English "taillight" is pronounced with one l or two l's: the point is moot, because English does not have the distinction.
깨끄타다 is correct way because ㄷ and ㅎ conjunctures.
1st step. 깨끗하다->깨끋하다 (음절의 끝소리 규칙)
2nd step. 깨끋하다->깨끄타다 (음운 축약)
The first step happens when the last phonology is not ㄱ,ㄴ,ㄷ,ㄹ,ㅁ,ㅂ,ㅇ and the latter word has a meaning. When the first step happens, the last phonology becomes one of the letters I mentioned above. As 깨끗하다= (깨끗+하)+다, and 깨끗 and 하 have meanings, 깨끗 becomes 깨끋.
The second step occurs when ㄷ, ㄱ, ㅂ meets ㅎ when pronounced sequently.
깨끋타다 will emphasize your opinion.
Also ㄴ,ㄹ,ㅇ,ㅁ have some difference with other consonants, as we wrinkle when we pronounce these consonants. So 충분하다 doesn't conjugate to 충부나다.