The Minchat Shai (by R Yedidya Norzi) at the beginning of Shlach says:
נון: במקצת ספרי' הנו"ן בדגש, וכן כולם. וא"ת כתב הנו"ן רפה, וכן חביריו
In some editions the nun has a dageish, and similarly the rest. And Or Torah writes that it doesn't, and similarly for the others.
Footnote 31 on Bar Ilan:
נורצי העיר על 'נון' רק בשתיים מהיקרויותיה, כאן ובבמ' לב כח, ובשתיהן שם דגש בדיבור־המתחיל. ונראה שנורצי מכריע שיש לדגש את הנו"ן.
Norzi only comments on נון two of the times where it appears, here and in Bamidbar 32:28, and in both places he puts a dageish in his דבור המתחיל. It seems that he's ruling that you should put a dageish in the nun.
I'm not sure which nun he's talking about, there are 3 of them in בן נון, but my guess is it's the middle one.
Based on the footnote the Minchat Shai preferred it with the dageish; every person that I've heard and recent chumash that I've seen goes with the Or Torah and doesn't put a dageish. For the editions that do have a dageish, why is it there? I've never seen one after a consonant besides for בגדכפת. How does this affect the word's pronunciation? Would you run the nun at the end of בן together with the one at the beginning of נון, as an exception to the general rule that we don't run words together (Brachot 15b)?