Welcome to the forum!
You mean these Document Properties and Preferences are Inkscape dialogs? I assume they are, but I'm not familiar with Mac or XQuartz, so I thought I should confirm it.
Would you happen to be using dual or multiple monitors? Or have you ever used more than one monitor on the computer where you installed Inkscape? We've seen things like this happen when someone was using more than one monitor. And they may have switched back to one monitor, but for some reason, Inkscape is opening them on the closed extra monitor. It is a bug. Changing your screen orientation could do it too (not Inkscape doc orientation, but your computer screen).
Another thing that might be happening, is that you have the dialogs docked. There is a way to sort of minimize a docked dialog (used to be called "iconified"), so that there's only a small bit of text to indicate it. So after you open one of those dialogs, look to the right side of the screen. That's the docking area. If it's minimized in the docking area, you'll see some text to the right of the docking area, which is written sideways, bottom to top. If you see the text, you can click on it, and the dialog will open. More info here on docked dialogs:
http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Anatomy.html and scroll down.
Or sometimes if you have the dialogs floating, they can open up somewhere outside the visible screen area. Or if the dialog is floating, and you minimized it (I mean the real kind of minimizing) it can be reduced to a tiny window somewhere along the bottom of the Inkscape window. It's so tiny that only the minimize, restore and close buttons can be seen. If it does that, it can be hard to notice. I think this has been fixed in current versions, but if you installed an older version, for some reason.
Document Properties and Inkscape Preferences are both such huge dialogs, that I suspect most people leave them floating. But it depends on what preferences you've set. If you double-click on any tool, in the toolbar on left side of the window, it should open Inkscape Preferences, to that tool. So try double-clicking on the Selection tool, and look around in any of these places, to try and find it.
