Some missions do have a time limit on the objective. Closely read your "orders" when you get them. Especially the "Lifeguard Duty" missions have specified dates for your boat to be "on station" for the mission. A few others do too, such as some of the photo recons. As far as a renonwn "penalty", a couple of the mods do that, but I don't think stock does. However, a "failed" mission objective does go on your permanent service record, and will be used against you in your court martial...
