In the Senate, only one-third of the seats are up for election. If those same states can't certify a Senator (apparently for the same reason they couldn't appoint Electors), the governor MUST appoint a replacement to fill the vacancy because Article V says "no State, without its Consent, shall be deprived of its equal Suffrage in the Senate." The Governor can choose to not appoint a Senator, leaving the state with reduced Senate representation.
And, since the entire House is up for reelection, there will be no House on January 3 to select a Speaker. More likely, the Republican states that do not use mail-in ballots will have ordinary elections and send their Representative to the House; they will not be affected by counting delays. It will be the Democrat states that can't count and certify their elections that will leave vacancies in the House. The Republican majority of those present will choose their Speaker.
-PJ
ha. Good one