I have been using SuperMemo for more than eight years and have more than 70,000 flashcards on a variety of subjects and languages, and once I got the hang of proper flashcard creation I have been able to remember almost anything I want: http://www.supermemo.com/articles/20rules.htm

Look at the above article for rules on how to make proper flashcards. SuperMemo, Anki, etc. are all good at helping you remember information, but if the flashcards are not correctly made, it's like putting water into an engine that requires gasoline. The thought that all explicit memorization is bad is a total myth; if you break any of the 20 above rules, flashcards will suffer (Trying to memorize before you understand, not learning things in list form, etc.).

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