When you limit yourself to "no holes" you also limit your threading options. I can almost guarantee you have water leaking into the cabin if you do use the door seal. The same goes for the trunk.
You didn't say what kind of antenna you were planning to use, but it sounds like a mag mount. Here's a couple of things you better know. First, most insurance companies will not cover any damages caused by a mag mount antenna. Secondly, using one will not save your paint. Read what I have to say about them on my web site.
Although you didn't ask, one responder mentioned the incoming power. This is easy on a Honda. Just to the right and just above the accelerator cable pass through, is a plugged 18 mm hole. It is easier to see from the engine side.