There is now some useful case law dealing with these issues - notably C-72/95 the Dutch Dykes case, C-431/92 the Grosskrotzenburg case, C-392/96 Commission v Ireland and C-435/97 World Wildlife Fund and Others v Autonome Sektion Provinz Bozen and Others (the Bozen case).
Inmiddels is er verhelderende jurisprudentie met betrekking tot deze kwesties, met name C-72/95 (de zaak Kraaijeveld), C-431/92 (de zaak Grosskrotzenburg), C-392/96 (Commissie/Ierland) en C-435/97 (de zaak Bozen).