Sacha: WRT your second question, there's a MUCH easier way: you can also use the heading title attribute to create a TOC entry sans any text (I do this all the time for illustrations); I wrap a header tag around an image, OR around nothing, thusly:
<h1 title="Put what you want in your toc here"></h1> , OR
<h1 title="This is Illustration 1"><img src=""></h1>
WRT to the whole TOC thing: I have had this problem myself, using hand-crafted ePUBs that I then imported into Sigil. The "problem" seems to occur when someone has created an ePUB and used headers for emphasis or formatting, and not specifically for structure, it seems to me...whereas Sigil "assumes" that you want every header item in your TOC (and gives you the ability to delete those items you don't want.)
And--if the toc.ncx that Sigil crafts from the structure is not the same as the hand-crafted TOC that uses bookmarks or anchors...yeah, your TOC gets "destroyed," so to speak. As I tend to work pretty exclusively in Sigil, I've only run into this a few times, so I haven't given a lot of thought to a simple (or not) workaround.