How can I exclude leads from receiving an email if they received an email in the last 5 days, but have them sent email later?

I don't think there is a good way to achieve this with a flow step because the "Not was sent email" filter needs to be set with a constraint of "in past 5 days". I would build your Target List in a Smart List of everyone you want to ultimately receive the email. Then, in your Smart Campaign, set the Smart List to "Member of Smart List in Target List" AND "Not was sent email in past 5 days." Send the email in that Flow Step.

Then build a separate Smart Campaign for "Member of Target List" AND "Not was sent email [the email you just sent]". In the flow step, send the email. Schedule this to run 5 days in the future. You'll also have to exclude these people from any other email sends in the next 5 days.

The short answer is, I don't think there's a way to have Marketo check every day for people from your Smart List who haven't received an email in the last 5 days and email them. You can use communication limits to make sure someone doesn't receive more than 1 email every 5 days, but not to eventually send them something they should have received.