If somebody borrowed my Teffilin, and then accidentally fell asleep while wearing them, and during his sleep experienced a nocturnal emission, have my Teffilin become spiritually damaged at all?!
Not a problem in the slightest. Pleae ignore it and continue to serve God by wearing your Tefilin. If this hangup is preventing you from doing mitzvos in a positive manner, please consult a competent rabbi and/or mental health professional.
Rambam, laws of Tefilin, Mezuzah, and Sefer Torah 4:13
וכל הטמאין, כולן חייבין בתפילין כטהורין
The incontinent are exempted from wearing Tefilin, but those who are ritually impure are all exactly as obligated to wear Tefilin as those who are ritually pure.
Similarly in 10:8.
כל הטמאים, אפילו נידות, ואפילו גויים--מותרין לאחוז ספר תורה, ולקרות בו: שאין דברי תורה מקבלין טומאה. והוא שלא יהיו ידיהם מטונפות, או מלוכלכות בטיט; אלא ירחצו ידיהם, ואחר כך ייגעו בו.
Anyone ritually impure -- even a menstruant woman or a non-Jew -- is allowed to hold a Torah scroll and read it, as the words of Torah cannot become impure. This assumes their hands are not dirty or covered with mud -- if so, they should wash their hands, and then may touch it.