How can I justify having only two publications when applying for postdoc jobs in physics/chemistry?
I do not understand why you find "weird" putting manuscripts in preparation in your CV. In my field, it is perfectly normal and accepted, and I guess in all academia.

This is the best way to explain what you did in the last years. It won't be strange at all, especially if you have talks on those results already, as you imply in a comment. These things happen; sometimes papers take a long time to prepare, and a selection committee should be aware of this fact.

It would look much weirder, in my view, if you don't list them and write a long statement in the cover letter about the lack of publications. As they said in ancient Rome, "he who excuses himself unsolicited, accuses himself".