When saying Kriat Shema Al Hamita, if one were saying all three paragraphs, would they said “emes” at the end? It seems to me that the reason we say “emes” is to attach it to the next paragraph, which wouldn’t seem to apply on Kristin Shema Al HaMita.
The Chabad custom is to repeat the words ה' אלקיכם and then also say אמת even during the Bedtime Shema, this is recorded in Sefer Haminhagim and also the Igros Kodesh. It's even printed in the Chabad siddur this way as well.
The reason is to arrive at 248 words altogether, corresponding to the 248 limbs as brought forth in Chatzkel's answer, quoting the Mishnah Berurah. Some people accomplish this by saying 3 words (א-ל מלך נאמן) before the Shema's 245. This however could be considered an interruption between the blessings before the Shema and the Shema itself therefore Chabad and others do it this way, by repeating the words ה' אלקיכם and saying אמת (see Kaf Hachayim OC 61:15 and ibid. 19, also Beis Yosef OC 61).