I think the absence of Harry Kane wouldn't really affect their performance in Bundesliga, I believe they can still able to win against Dortmund. As long as Muller and Musiala are playing, they don't have to worry against mediocre teams.
But when it comes to Arsenal in Champions League, I'm not convinced Bayern Munich will win. It's The Gunners games because the match will held in Emirates Stadium.
I think these two teams are not easy for Munich to face, Borussia Dortmund is not a mediocre team, it is a top team in the Bundesliga, the same as Munich, so the absence of Harry Kane will definitely really affect Munich in the upcoming match, and what is certain is that Munich's attack without Harry Kane will be a bit decreased because Harry Kane is a goal scoring machine for Munich so I'm not sure Munich will be able to win the match against Borussia Dortmund later.
So, that is Munich's problem at the moment, even though Munich wants to fight harder in the UCL to get a trophy, but if one of the important players is absent, it will definitely be very difficult for them.