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The Boondock Saints (1999) More at IMDbPro »

Although the film never explicitly states it, its pretty clear that Agent Smecker is gay. He would be what is referred to in the gay community as a SAG (Straight Acting Gay) but the fact that he is intimate with another man in the film is pretty clear evidence. The use of the word 'fag' is most likely just his reaction to his partner being too affectionate.

To put it simply the Unrated version features several extended action sequences and bloody shootouts that are missing in the R-rated version of the movie. You can find a detailed comparison between both versions with pictures here.

Yes, he is their father.

Il Duce was hired to kill the two vigilantes, however, he didn't realize that they were his children, nor did Connor and Murphy realize that Il Duce was their father. It wasn't until Duce was about to ambush them at the end, that he overheard them saying their family prayer. Which Duce obviously realized would be too much of a coincidence for someone else to know it. Also he probably knew he fathered two sons.