R. Aryeh Kaplan, in his article "Reverence of the Sacred," writes that י-ו is written as טז, not because it's a divine name (unlike י-ה, which Avot DeRabbi Natan 34:2 and others write is actually a biblical name of God). Rather, its lettering is changed because י-ו "resembles a divine name."
This exemplifies our sensitivity to desecrating God's name (other examples include writing BeSiyatta DeShamaya in correspondence or writing Yehudah with a final Aleph - "lest one accidentally leave out the letter Daleth and write the Tetragrammaton").
As for the examples that you mention, it's important to remember that biblical names with weak letters are often abbreviated, but when written in full, י-ו become י-ה-ו names, which definitely include a biblical name of God. For example, in II Sam. 1:22, Yonatan is fully spelled יְהוֹנָתָן and in 2 Chron. 28:12, Yochanan is יְהוֹחָנָן.
Thus, such names commonly spelled with י-ו refer to Hashem because their "full" names include a divine name, י-ה.