The Spanish use of y vs. e and o vs. u can be classified as an example of sandhi and dissimilation.
Sandhi is a pronunciation change caused by contact between words (or morphemes), usually in a way that can be thought of as making the pronunciation "easier" in some way.
Dissimilation is a change of two similar sounds to less similar sounds.
Your other two examples in my opinion are probably coincidences.
German and -en
Männen is not a plausible plural form of Mann as no German noun forms its plural with umlaut and the suffix -(e)n. Umlaut in the plural is associated with the suffix -er or the ending -e or -∅ (German noun plural reconsidered Dieter Wunderlich,University of Düsseldorf, April 1999; The grammar and typology of plural noun inflection in varieties of German Richard Wiese, page 3).
Mannen is more plausiblenot completely unprecedented the way that Männen would be, but in generalstill, it is not a particularly likely plural form to begin with because the German plural suffix -(e)n is associated regularly with feminine nouns, and occurs only sporadicallyinfrequently on non-feminine nouns. Because Mann is not feminine, there is no particular reason to expect Mann to form its plural with -en, so the fact that it doesn't end in -en is not very significant as a strong sign that German avoids using -en after n. In fact, we do find -en after n in a number of German plural forms such as Allusionen or any word ending in the feminizing suffix -in (plural -innen).
English be
The irregular forms of the verb be have a long history that makes it seem unlikely that the present-day forms of the pronouns specifically influenced the use of is as a form of be.