The following are some sections quoted from the Shlchan Aruch HaRav. I did not included everything in the text nor all of the footnotes but the sources for which the entire sections can be found are listed at the top before the smaller sections from individual paragraphs are quoted. It seems that the main two reasons have to do with the soul departing from the body, a spirit of impurity that rests upon a person when the soul leaves the body, and the possibility that our hands may have touched any part of our body which would normally be covered. One of the footnotes gives a source that discusses a person who sleeps or naps during the day but I don't have access to it.
Shulchan Aruch HaRav: Laws Relating to Rising in The Morning (1:1-1:19)
Paragraph 6:
"... Since this statement does not include any of the 7 Divine Names (48) that may not be erased, one is not forbidden to recite it before washing his hands. This applies even when he slept naked and his hands presumably touched unclean parts of his body, as will be explained in section 4.
note 48: The Rebbe points outt in Inyaneh shel toras HaChassidus that the recitation of Modeh Ani was instituted after the Talmudic era. In Talmudic times, people recited the blessing that begins Elokai Neshamah immediately upon rising, b/c at that time they "were holy and could recite a blessing in purity immeditalt upon rising (Rabbeinu Yonah, gloss to Berachos 60b)
Paragraph 7: As explained in the Talmud (berachos 60b) and subsequent halachic authorities {Rambam, hilchos tefillah 3:3, 4:1; Rosh (on Berachos, ch 9) Sec. 23} rule that when a person sleeps in his clothes, it is possible that his hands did not touch the unclean parts of his body; (as the Alter Rebbe writes in his siddur, the parts of the body which are normally covered 92:7) hence his hands are presumably in a sate to speak words of Torah (Rama 47:13)...he should merely refrain from touching food or drink, as explained there. (Rashi on Yoma 77b) Nevertheless, the Zohar (intro page 10b & in parshas vayeishev p 184b) rules very stringently that one should neither recite blessings, nor study, not touch one's garments(53b), nor walk(Eshel Avraham 4:1. also see likkutei sippurim by R. Chaim Mordechai Perlow p. 287) four cubits while the spirit of impurity still rests on one's hangs before they are washed in the morning. A person who walks 4 cubits before washing is liable for his life, for by allowing this impurity to rest upon his hands, he desecrates the sanctity of G-d which rests upon him..."
Shulchan Aruch HaRav: Laws Relating to Washing the Hands: 4:1-4:2
Paragraph 1: Our Sages ordained that one should wash his hands with water every morning and recite the blessing AlNetilas Yadayim, (berachos 60b) The rationale for this ordinance is explained by some (Rosh, Berachos 9:23; Rmbam, hilchos tefilla 4:1) as preperation for the morning recital of shema and shemoneh esrei, for the hands are active (from the responsum of Rav Amram Gaon) and probably touched unclean arts of the body during sleep..."
"...but for the reason explicit in the Zohar (arshas Veyeishev) and also mentioned in the Talmud (shabbos 109a) to remove the spirit of impurity that rests on the hands and that results from the withdrawel of the soul's holiness from the person's body at night when he is asleep. (as to one who sleeps by day see mahadura kama 4:15 also 55:8). The washing enables the erson to sanctify himself in G-d's holiness (responsa of the Rashba vol 1 sec 191; Rokeiach sec 363) by the pouring of pure water from a container..."
Paragraph 2: In the Talmud as well (shabbos 109a) the Sages cautioned about this spirit of impurity that rests on a person's hands upon awakening, saying that it is not removed until he washes them three times, alternately, (shaar Hakavanos, inyan birkas hashachar). THey also warned (shabbos 108b) that before washing one should not touch his eyes, ears, nose mouth, anal opening, any place where he has let blood, or his organ - i.e., from the corona and below, or for the purpose of relations. Nor should he touch water that was prepared in a tank to enable all the members of his houshold to wash, so that his hands will not make it impure.
