Schachter and Shopen (p.59) have the following to say:
The last closed parts-of-speech class to be discussed is the class of politeness markers. These are words which are added to sentences to express a deferential attitude toward the person addressed. In Tagalog, for example, there are two politeness markers, po and ho, either of which may be added to any sentence the speaker wishes to render polite. (Po is more polite than ho; to borrow the terminology of Kuno (1973), po may be called ‘superpolite’.) In some other languages, such as Japanese, the expression of politeness involves, instead of markers, a special polite vocabulary: for exam- ple ee ‘yes (polite)’, hai ‘yes (superpolite)’ vs un ‘yes (informal)’; boku ‘I (polite or informal)’, watakusi ‘I (polite or superpolite)’ vs ore ‘I (informal)’. (Japanese also has a special polite affix, -mas-, which is added to a verb in polite speech: e.g. ake-mas-u (open-polite-present) ‘open (polite)’ vs ake-ru (open-present) ‘open (informal)’.) The use of special polite forms for ‘you’ is particularly common: for example Spanish usted ‘you (polite-singular)’, ustedes ‘you (polite-plural)’ vs tu ́ ‘you (informal-singular)’, vosotros ‘you (informal-plural)’.
Schachter, Paul & Timothy Shopen. 2007. Part-of-speech systems. In Timothy Shopen (ed.), Language typology and syntactic description, vol. 1, 1–60. 2nd ed. Cambridge: Cambridge University Press.
I don't see why, based on that sort of broad description, we would not expect some languages to have affixes rather than independent words.
Edit: The Kuno reference is:
Kuno, Susumu. 1973. The Structure of the Japanese Language. Cambridge, MA: MIT Press.