You can still get to Hakone Yumoto station. All trains to Hakone are running. However the Tozan railway has sections totally gone so it won't be repaired until next year. Lake Ashinoto is overflowing at the moment so no ferry services are available until it returns to normal water level. Many road sections around Hakone are closed so you will need to check for road closure information if you are driving. Apparently many of the normal tourists sites are still open - Tenzan onsen, the open air art museum, etc.
For more info, check Hakone town homepage
http://www.town.hakone.kanagawa.jp/