Bayern Munich's substitutes are also strong enough. And they have the ability to beat any team. However, they are a bit weaker than the main squad. I'm not saying Bayern Munich will lose with a second squad. However, if the opponent is strong, it will be very difficult for Bayern Munich to win with the second squad.
If we look at every player of Bayern there are so many notable players to think of, and I know what you are saying but I am not considering grouping them as a 1st squad and the 2nd squad, all players do have a skill they are good at, whether it is for the offensive or defensive purpose each player of Bayern Munich is needed, well the notable goals scorer for Bayern other than Lewandowski are Serge Gnabry, Thomas Muller, Leroy Sane, Joshua Kimmich, Dayot Upamecano, Kingsley Coman, Marcel Sabitzer, Leon Goretzka, and Jamal Musiala pretty much there are many well-known players for Bayern and I think this roster is a powerhouse even if they don't have Robert Lewandowski.
I am quite sure that Bayern would still be the by far biggest favorite for the Bundesliga title and also one of the top candidates to win the Champions League even if Lewandowski would leave the club now. His back up player at the moment is Choupo-Moting who is also a great striker and always performs great when he has a chance to play. Also if Lewandowski would leave the club now, they would buy a proper replacement for him too. Bayern had to play a few games now without Kimmich and Goretzka and they still one and i would say that missing both of the midfield strategists at the same time is more severe than missing 1 striker.
I didn't include Eric Maxim Choupo-Moting maybe because he is not available until December 31 to play, but there is much replacement for the team of Bayern Munich, and if Robert Lewandowski decided to leave Bayern surely have the financial stability to gain a player with the same caliber as Lewandowski.