Is there a disadvantage to the "fan in fin" design seen for the tailrotor on many Eurocopter helicopters?
The fenestron is a lot heavier than a free tail rotor. This is probably the main disadvantage; helicopters are more sensitive to extra mass than aircraft.

At the time Eurocopter was produced by joining Aerospatiale's and MBB's helicopter divisions in 1992, a follow-on to the successful Bo-105 was under development. That was the Bo-108. Immediately, development was stopped to implement a fenestron into the finished design in order to give all Eurocopter products a common, distinctive feature. This resulted in major structural changes and a heavier helicopter. The result is now known as the EC135.

From this Aerospaceweb article:


  The only significant drawback to ducted fans like the Fenestron is
  that the shroud adds weight that offsets at least some of the
  improvements in performance.


As @Koyovis' answer points out, the low position of the lateral thrust vector is also a clear disadvantage. See here for more.