The votes are only meaningless in terms of delegates. They are still votes.
They count in a popular vote total.
They could have voted by write-in for Oscar the Grouch. If so, Someplace, there should be a list of votes with one vote for Oscar the Grouch.
They count in a popular vote total.
The candidates aren't elected by direct popular vote.
The primaries in those two states were basically unofficial, the value of those votes means as much as a poll would.
If you want to count them in your version of the popular vote, I guess you can go ahead, but as far as the National Democratic Party is concerned, they aren't official votes. The state may have certified them as official as far as the state is concerned, but they don't make the rules for the national party.
I guess our whole argument is rather academic. The superdelegates are going to decide however they choose to decide. They are under no obligation to be swayed by anything but their own choice. If they feel the votes in Florida and Michigan are significant to them, then they are. If they decide they aren't then they aren't.
If counting the votes for Hillary in Michigan and Florida gives Hillary the lead in the popular vote, then I'm sure some superdelegates that vote for her will give that as a reason for doing so regardless of it it's true or not.