Yes, the most practiced religion in the western world has had a large influence on the names people living there give their kids. You're mostly right, the original versions of those names were very different (though they're mostly Hebrew and Aramaic, not Arabic, which didn't exist until well into the first century AD at the earliest, although they are all part of the same family of languages), and in most cases went through several other languages before reaching the names we know now.

Please note that there is still some dispute as to the exact transliterations and etymologies of some of these names, I'm giving the ones I'm most familiar with.

For one example you mentioned, John, a common name in numerous western languages, comes from the Latinized version (Iohannes or Johannes), of the Greek translation (Ιωαννης, Ioannes) of the Hebrew name יוֹחָנָן (Yochanon, among other transliterations, meaning 'God is gracious').

You can trace a similar path with Jesus, which is the Latinized form of the Greek translation (Ιησους ,Iesous) of the Aramaic name יֵשׁוּעַ (Yeshua), which was itself a shortened from of the Hebrew (יְהוֹשֻׁעַ, Yehoshua, 'God is salvation'), which is the same route we get the name Joshua from.

Same with Mary: Mary being a shortened version of the Latin Maria, from the Greek Μαρια 'Maria' and Μαριαμ 'Mariam', from the Hebrew מִרְיָם 'Miryam'. Rebecca is much the same, being from the Greek Ῥεβέκκα, from the Hebrew רִבְקָה 'Rivkah'.

Paul and Mark are the odd men out here, as they were Romans, with Latin names, Paul coming from the Latin word paulus, meaning 'humble', and Mark a shortened from of the Latin Marcus, derived from the Roman god Mars.

As for your question about whether Yeshua was a common name, it seems to have been reasonably so. Jesus of Nazareth wasn't the only Yeshua held by the government at the time. The full name of Barabbas, the man whose sentence was commuted, was ישוע בר אבא, Yeshua Bar Abba.