For me, the ropeway is a good part of the fun of visiting Hakone. There is apparently an alternate bus service to get around the closure but it isn't the same.

As to the museums, and I include the outdoor sculpture/art museum that is the most famous, they don't come across to me as worthy of a visit. There are a whole lot of junky museums -- The Little Prince museum, really? -- mainly there to sop up money from a Japanese crowd.