The relevant phenomenon is called 수의적 경음화 or 수의적 된소리되기, which the pronunciation rules cover only partially. 수의(隨意) indicates that the phenomenon has no regularity. There are no rules that explain directly why 권 of 여권(旅券) has to be pronounced as 꿘 (Ref. 1). Part of the answer in Ref. 1 says:
언중들이 '여'와 '권' 사이의 형태 경계를 인식하여...
meaning "It seems that language speakers suppose that there is the morpheme boundary between 여 and 권". It could be one reason because one of the rules says:
표기상으로는 사이시옷이 없더라도, 관형격 기능을 지니는 사이시옷이 있어야 할(휴지가 성립되는) 합성어의 경우에는, 뒤 단어의 첫소리 ‘ㄱ, ㄷ, ㅂ, ㅅ, ㅈ’을 된소리로 발음한다.
regarding the implicit 사이시옷 that you mentioned and morpheme boundaries of compounds. 여권 is, nevertheless, not 합성어 (a compound). -권(-券) is used as a suffix for a lot of words (관람권, 상품권, 입장권, 승차권, ...). A suffix can be contained in derivatives. Maybe the rule makers forgot to consider that some derivatives also follow that fortification rule.
Well, I must say that not every person tries to figure out or care about the logic when they use their native language. We learn the pronunciation as we hear or listen to what others say. Where almost every person pronounces 여권(旅券) as 여꿘, 여권 is extremely unlikely to be accepted as the correct pronunciation. Such a phenomenon might relate to language speakers' preference. At least I can say that this is a thing you should just accept and follow.
These examples show the irregularity in the pronunciation of 권(券) (Ref. 2).
권(券) is pronounced as 꿘: 차권(借券), 채권(債券), 위권(僞券), 문권(文券), 신권(新券), 승선권(乘船券), 교환권(交換券), 입장권(入場券), ...
권(券) is pronounced as 권: 전권(典券), 지권(地券), 가권(家券), 환권(換券), 고권(故券), ...