Did Wisconsin ballots have any special encoding with invisible watermarks or blockchain codes?

No. One of the stranger claims after the election was that legitimate ballots had been specially encoded by one of the political parties so any illegitimate ballots could be rejected.

Wisconsin county clerks are responsible for printing ballots which are distributed to municipal clerks. The secrecy of your ballot is safe. Clerks do not print any watermarks or codes on them that would identify any voter or political party. Ballot anonymity is a requirement of the law, and what candidate a voter chose is not a part of their record.  The state of Wisconsin also does not track party affiliation.  Local election officials do not know voter’s party preference when issuing ballots.