Do you take Latin, or have you taken Latin? You are correct that filii is a plural nominative. However, the form filii is also the genitive singular. If you are not familiar with the complexities of grammar, the genitive case is the form of a word which is possessive. In this case it is “In the name of the Son”. Since the Son possesses the name it goes in the genitive. At first, when I read your post, I thought you might be right because many times second declension nouns drop one of the i’s in the genitive form. This would make the word fili. I looked on the internet and found people using both the form fili and filii. Not sure whether it was a mistake in my original Latin Mass source or not, I opened up a Latin Missal and found that it used the form filii just like my original. Therefore, I will assume that filii is the correct form. It is possible though, that a discrepancy exists between Ecclesiastical and Classical Latin. I can’t verify this though. Have you seen the form fili used instead, or what prompts this question?
On another note, have you ever gone to a Mass? Have you been to a novus ordo missae (modern mass in the vulgar tongue), missa romana (traditional latin rite mass), or both? If you have, then I am interested in knowing your thoughts concerning the differences between the two.