I use those tags and I think they're necessary. For someone who hasn't read the work in question, they don't know, ahead of time, if the text of the question will spoil something for them or not.
It's true that sometimes the title itself can spoil something for people, and in that case, it doesn't help to mark it, but there are reason for marking a title with [SPOILERS]. (And, honestly, I think it was inappropriate to go through and delete all those warnings **before*8 bringing this up for discussion.)
I've had books and movies I haven't finished spoiled for me in the past. One case was someone posting, without warning, the last sentence from _Deathly Hallows) in a forum that wasn't even about Harry Potter. We've all had works spoiled that way in the past.
As for the using markdown notation instead:
There are problems with spoiler markdown. Just try to write two paragraphs in spoiler notation and see what you get.
User education is an ongoing problem and not everyone knows how to uses the spoiler markdown format and, honestly, not everyone will learn it.
As of now, the markdown help page that appears while writing posts does not include how to do spoiler tags.
For many people, this will be a lesser used feature of the markdowns, and when people don't use a feature too often, they forget it or forget to use it.
On any site, you have to remember you can't control users. There will be some that do every little thing right, but that's a minority. But there's always a good number that won't learn details like spoiler markdown.
You haven't made a case that using [SPOILER] in a title of a question is harmful. At this point, I'm not sure if it's a site policy or just a personal preference.
There are many times a person is involved in reading or watching something and is interested in the question, wondering if it'll explain a question they already have that might be a plot oversight or intentional, so they want to see if a posted question will help.
Sometimes the entire question would need to be in spoiler format, which almost always leads to a human impulse to at least see if that's a mistake.
This is an essentially harmless and can help people enjoy their reading/viewing and enjoy this site more by providing a quick and simple way people can announce spoilers without having to learn markdown (and some people don't know any markdown tags and don't want to learn).
It's pointless to ban something that doesn't do harm but can prevent harm. The bottom line is the site is here for the benefit of the users, not the users here for the benefit of the site. If the users tend to do something one way, that indicates that's what they prefer.
