I prefer my books without indents and with blank lines between paragraphs. Just easier for me to read due to the smaller page/line width of most ereaders.
I used to think I was in a very small minority group, but now it seems that half the books I read are formatted this way to start out with.
I am not fanatical about it, often I will change the book, but if I find myself reading one that I haven't changed I just carry on usually. I do notice it often enough throughout the book that I can understand the irritation some might feel if they prefer otherwise.
I literally never noticed in paper books especially mass market. Didn't bother me one way or another which is good as no way to change them
I personally feel that the overall quality in ebooks has improved immensely in the 3+ years since I got an ereader. My first ebooks from the library had page numbers and page headings mid page and big old gaps following them and were only reflowable to a limited extent. Many (most) public domain books were butt ugly, some with weird typewriter fonts etc. Still more than a few like that, but I haven't encountered any recently.
Reading on a tablet, which I rarely do, I actually don't notice those pesky indents and lack of spaces. Strangely they irritate me on a desktop or laptop.
As for self published, most possibly do them according to their personal preferences, although I am pretty sure a few of them have rarely read a book let alone their own.
Helen