How can i get doors in my house and ships so that they can be more protected?

You need to get a ToolKit, equip it to one of your hands and stand in an entity with more than one room. Then you go to 'Room Travel' and then 'Actions' where you will find a button named 'Locks'.

Install times;
Standard door: 4 Hours
Reinforced door: 8 Hour
Blast door: 12 Hours

If you pass the skill check :)