Aizi24 - those are called tooltips and balloons help and you're right, they have been around for awhile. Balloon help first appeared in Apple's OS around version 7. Tooltips are usually a small bit of information related to a button, etc. Balloon help was more information again used for help, like how a function worked in MS Word.
Tooltips remain but balloon help has slowly faded away simply because it's too intrusive.
Wikipedia's implementation is not a tooltip, it's more like balloon help on steroids.
You're using your particular needs - having your own wiki and editing it - and applying it to Joe public. It's really not the same thing at all. Sounds like for your needs it is pretty handy but for someone who just wants to read an article it's intrusive.
"...button nearby the hyperlink is not a good idea because that will extremly disturb the reading process of the article text."
If you read the complaints that is exactly what people are annoyed with, how it extremely disturbs the reading process of the article text. Without focusing on your curser at all times (tracking your cursor changes the very way one is browsing through an article) these can popup by simply coming to rest over a link.
For the average user having control of that popup would give them control without having to turn it off if they're annoyed by it. A small button (like a ? button) would put control in the users hands. It's the only solution whereby the feature can be used by everyone.
People who don't want it don't necessarily think it couldn't be useful, they don't want it specifically because it's annoying. I can certainly see its usefulness and would use it but as is it's too annoying to use for me. I want to use it - and this is a key arguement - ONLY WHEN IT'S USEFUL. When it's not it's just annoying.
Wikipedia is saying it's either on or it's off.
And no other content delivery site functions like this. You wouldn't read a WSJ article and expect to have to focus on where your cursor is at all times so you can avoid things popping out at you.