Any mod that overwrites the commands.cfg files and has not already been made compatible with Integrated Orders will break Integrated Orders. It modifies the commands.cfg files and those modifications need to be there in order for it to work properly.
If you want to use DD's Open Hatch mod (or FM New Interiors, for that matter) and keep Integrated Orders you will need to follow the instructions included with the former and manually add the necessary changes to your existing commands.cfg files (the versions of them that Integrated Orders uses) rather than overwriting them entirely.
When using JSGME to enable mods, it should tell you when a new mod is going to overwrite a file that has already been changed by a previously enabled mod. Sometimes this is okay, as there are mods that are designed to work with other mods and in those cases the additional overwriting of shared files may not be a problem or may even be necessary for both mods to work together. If so, it will usually mention this in the documentation for the mod (or in the thread devoted to it here if there is one).
But if you get an alert from JSGME that a mod is going to change a file that another mod already changed, and you weren't expecting it or don't know whether or not that will be problem, that's the time when you need to cancel out what you're doing and make note of what files are involved so you can investigate further until you know whether or not it's going to be a problem.
FM New Interiors also uses a modified Sh3.sdl file, which will already have been modified (in your setup) by Lifeboats & Debris. Aces has a mod that gives you an Sh3.sdl file that combines everything necessary for both mods (plus a few other popular ones that use the same file) so you will want to get that compatability fix if you decide to use both.
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