Not everything that is important enough to write down has the same importance. While the phrase may be over-used, it is merely one in a long range of methods we use to draw more attention to statements we believe have particular importance at a specific point.
If the statement is not genuinely something that needs particular attention, then I agree that such phrases should be avoided.
However Wikipedia's policies in are not particularly relevant here, as in the case of an encyclopaedia which pieces of information are important depends entirely on what the reader is looking for at any given moment - the purpose is to make the information available, not to direct the reader to pay special attention to particular bits of information.
In many other contexts, the purpose of the text is not to merely make information available, but to influence the reader, and in many cases to specifically draw their attention to specific pieces of information. E.g. consider safety instructions or documentation of something where there are serious caveats.
In those situations various forms of emphasis are important, and using specific phrases to convey that a given statement is more important can be one valid way of creating emphasis.