Either that, or "Namco X Capcom" needs to be "Namco Cross Capcom", "Sengoku Basara X" needs to be "Sengoku Basara Cross", etc.
The reason for this is that "Dot Hack" is a pronunciation of the actual written title .hack (with the word hack intentionally lowercased every time) just like "Namco Cross Capcom" is a pronunciation of the actual written title "Namco X Capcom". ナムコ クロス カプコン, the クロス is "kurosu" which is cross. So we're using the written title in one case and the pronounced title in another. It doesn't make a whole lot of sense this way.
Unless we want to change X to Cross in all those instances... which I think is kind of stupid since that's not what's actually written... then we should just write what's written and put .hack.
Also yeah the capitalization is very purposeful, it's .hack//TITLE for the NTSC-U/C releases (whereas for NTSC-J it's .hack//Kanji so no capitalization for the second part, but it's still always lowercased .hack and that's across all different .hack titles).