Avoid having items on your bike that are out in plain sight, those are the only things that have gone missing for me. By that I mean things tucked under the straps or whatever.

Keep the most theft worthy stuff with you, credit cards, phone, money... The rest is just dirty clothes and and used camping gear

I typically leave my panniers loaded and on the bike for just about my whole tour. I try to avoid big cities as much as I can and am inclined to get a room if I stay in over in a big city and don't have a host. I figure that it is possible that at some point it could all come up missing. For that reason I like to have a bike and gear that I can afford to replace if necessary.

The more bike friendly the city the more careful you need to be. Bike friendly cities tend to have bike theft as a cottage industry. Stick to rural and remote small town areas and it will be mostly a non issue.