On the 'other' door, a narrow piece of angle, or channel will prevent a jemmy being used against the weatherstrip. If you can't weld this, then you can drill/tap/screw to the steel (and fill over the screw heads).
I can't offer any suggestion on the hinge sides, except, as you say, a snug-fitting hard rubber strip to close the gap.
One question, though, where is your boat to be moored? Marina, online public or offside? I ask this because there are likely two? types of thief about - the opportunist, who will not tackle anything that doesn't look easy, and the one who thinks - Ah! bloody big padlock, must be something worth having in here!
If you must use a padlock, then a 'disc' type or similar is best so that they can't get in with bolt croppers, but hasp/staples can be cut unless you use a sturdy cowl/cover. One of my friends uses only a decent mortice lock on the stern doors, all other security is built inside (bars), except the weatherstrip protection.
Think about protection for your slides, too!
Fit a flashing LED at each end of the boat - the thief will not be sure what it means and move on. This was the case when both my friends boat and mine were on the same online public moorings - other boats were attacked, ours weren't. Put a radio and a lamp on a timer for the dark hours.
How far should one go?