I've used it for 8 months, and did not observe any negative side effects in the nature of those you mention.

One thing that I would consider somewhat of a disadvantage of an explicit repetition system is that you need to really take care of how you engineer the questions to match the way you would normally encounter the knowledge they refer to in real situations.

For example, read the section on "Two-way connections" of this article, also linked somewhere else in this thread: http://rs.io/2014/04/05/anki-10000-cards-later.html