Why is the Nun in Menasheh suspended (above the other letters)?
Rashi (from Bava Basra 109b): It is due to Moshe's honor (the verse does not explicitly call him Moshe's grandson). It is written suspended to teach that really, he was not Ben Menasheh, rather, Ben Moshe. 1
Radak: [Yehonason] is attributed to Menasheh, for his actions were like Menasheh's.
To which Galus does the verse refer?
Rashi, from Yerushalmi Brachos 9:3: It is the first exile [of the 10 tribes] via Sancheriv. 1
Radak: It is until the Aron was exiled, about which it says "va'Yitosh Mishkan Shilo...; va'Yiten la'Shevi Uzo v'Sif'arto v'Yad Tzar; va'Yisgor la'Cherev Amo", "va'Yach'isuhu b'Vamosasm uvi'Fsileihem Yakni'uhu" (Tehilim 78:60-62, 58); verse 58 refers to Pesel Michah. Verse 31 supports this - "Kol Yemei Heyos Beis Elokim b'Shilo." Presumably, these times are the same. Shmuel, even though he was a Shofet [in the days of Eli, before Gelus ha'Aron], did not protest, for he did not want to publicize his authority due to Eli's honor. Eli did not protest, just like he slackened from rebuking his sons. When Eli died and the Aron was exiled and many Yisraelim were exiled and many died, the Pesel was abolished.
QUESTIONS ON RASHI
Rashi writes that [they were Kohanim] until the exile [of the 10 tribes] via Sancheriv. How can it be that David and Shlomo did not abolish Pesel Michah?!
Radak (Shmuel II, 21:2 citing Rav Sadya Gaon): During the famine towards the end of David's life; he eradicated everything that he found of Pesel Michah. (This implies that there was a remnant that he did not find. - PF)
Malbim: In the days of Shmuel it was abolished. Regarding this, it says Kol Yemei Heyos Beis Elokim b'Shilo. Yehonason repented, and David appointed him over the treasury (Yerushalmi Sanhedrin 57a). In the days of Yaravam, he set up the Egel in Dan, and Yehonason's sons were Kohanim until the exile via Sancheriv. 1