Was Jefferson’s character a big issue in the 1800 election in a similar manner to Bill Clinton’s character being an issue in 1992, 1996, and 2016?
Indeed, and very similar to Clinton's scandals too. The Hemmings affair wouldn't come out until after the election, but at the time there was much made of Jefferson's supposed cowardice during the War of Independence, when he fled Monticello to evade capture by Benedict Arnold. There were also rumors, spread by the Federalist presses, that Jefferson was the "mean-spirited son of a half-breed Indian squaw and a Virginia mulatto father" —which
we wouldn't consider a character flaw, but people at the time certainly did.