There are two elements you need to consider with regard to this qustion - laws and people. Some countries have laws about what you can photograph and those laws apply not only when you set foot in the country but also when you fly over and when you are in a plane registered in that country (and bear in mind that you may have a ticket saying this is an "XX" airline flight but you are actually on a "YY" plae).
But you also have to deal with people. Here in the UK the general rule is that so long as you're in a public place you can photograph what you like. I took a picture of a block of flats which happened to have someone walking past. He came over and told me I couldn't take his picture (he said it was against the law) so I explained that he was incidental to what I wanted to photograph and the law allowed me to do it anyway. As a passenger on a plane I would probably "keep the peace" if someone objected (passenger or crew) and not take photographs, you really don't want things to get nasty in flight. In any case, so long as you are shooting digital, it should be possible to recover any deleted images so long as you take no more photographs on the card that images have been deleted from.