Ever since a friend with a single fem profile showed me her KS homepage with literally thousands of notifications and hundreds of unopened mail, no, I don't consider it rude/impolite to not reply to messages even when genuine and thoughtfully-crafted.
I think this boils down to an issue of perspective where the KS user experience between men and women is so hugely different that they can't be compared. Female-owned profiles get SO MUCH unsolicited engagement.
Hell, just look at the ratio of likes between pics posted by men and women - it's common for women to get 50+ likes and multiple comments on a pic after a few days - who knows how many private messages that translates to. I couldn't imagine managing that much engagement! It seems pretty easy for one genuine message to slip between the cracks, or, honestly, seeing it but not having the energy to engage with it.
Even when you've read a profile and taken the time to craft a thoughtful message, you need to accept that yours could still be the 100th message received that week. As others have said, no reply or leaving you on 'seen' is still a reply and no one is entitled to a response no matter how nice/relevant their message is. It is what it is.
Don't take it personally, just move on and you're that much closer to your next encounter.