Your regex works for me:

$ cat foo
ironia/ironia/S-FS  (/(/PU  lo/lo/PQMS  soprannomineranno/soprannomina
+re/V-P3IF  "/"/PU  Pique/pique/SP  la/lo/RDFS  lune/luna/S-FP  "/"/PU
+  a/a/E  causa/causa/S-FS  della/di/E-FS  forma/forma/S-FS  del/di/E-
+MS  suo/suo/A-MS  naso/naso/S-MS 
$ cat foo | perl -pe "s/-\w{2,}//; "
ironia/ironia/S  (/(/PU  lo/lo/PQMS  soprannomineranno/soprannominare/
+V-P3IF  "/"/PU  Pique/pique/SP  la/lo/RDFS  lune/luna/S-FP  "/"/PU  a
+/a/E  causa/causa/S-FS  della/di/E-FS  forma/forma/S-FS  del/di/E-MS 
+ suo/suo/A-MS  naso/naso/S-MS
[download]

If you want to modify the file in-place, take a look at the -i switch

Update: I didn't notice that you want to delete all occurrences. ikegami++