My suggestion is to be courteous with your auto-farms and don't lag other players just because you want to be greedy. Don't set them on timers, use a button to activate it instead.
1) Collecting resources while alt-tabbed is no better than duping, which is a banable offense.
2) If you forget to deactivate your auto-farm it runs constantly and wastes server resources other players might need.
3) If you're too lazy to press a button then you should get off Minecraft and reevaluate your emotional condition.
...and yes, boats lag the server so if any mod finds an auto farm using boats I believe they've been instructed to "break" it and warn/notify the owner. I think this rule should also apply for any auto-farms that are active when a player is offline/afk.