1) Many of us have also seen the C++ library or application that busts out the template metaprograms at every opportunity. Haskell is the same. Use restraint when bringing in new libraries and programming techniques. (as an aside, I have yet to encounter a single problem that I thought merited the use of arrows)
2) You also see this in other languages, though to a lesser degree. The same techniques we use with other languages work just as well in Haskell: As leadership, form a strong opinion on the best way to write control flow and ensure that everything uses a consistent style.
3) Are your engineers running around implementing random research papers? This has nothing to do with Haskell.
4) In practice, this is almost never a big problem. Refactoring a pure function to an effectful function is easy and safe. In a production setting, almost all of your functions run in some monad already, so it's pretty rare to run into a situation where you suddenly need to percolate effects through many functions.