First of all, all tools may be helpful but not reliable. No tool can produce a reliable vocalised Arabic text from an unvocalised one. They can help to reduce the typing and manual input effort but it all would have to checked by a knowledgeable human. No harm in researching, though.

Vocalised Arabic is used in religious texts, especially Qur'an, otherwise, the usage is very similar to Japan's furigana, mainland China's pinyin and Taiwan's bopomofo (zhuyin fuhao). I possess a few vocalised readers, dictionaries and textbooks. Noteably, Oxford or Larousse Arabic dictionaries, Russian author Ilya Frank's Arabic Joha adventures book, Lingualism pdf bilingual books in MSA have full vocalisations and audio.

On various level's vocalisation. Let's say, we want to write "the large book" - الكتاب الكبير (al-kitāb al-kabīr), also al-kitābu al-kabīr(u) or al-kitābu l-kabīr(u)

1. Full vocalisation in the nominative case can be الْكِتَابُ الْكَبِيرُ - al-kitābu al-kabīru or al-kitābu l-kabīru with markings for cases - ʾiʿrāb - https://en.wikipedia.org/wiki/ʾIʿrab. This can be even more pedantic with الْكِتَابُ ٱلْكَبِيرُ, marking the first alif in the second word as silent (a less common diacritic). The final vowels used in the ʾiʿrāb is often omitted for various reasons. Vowels are often unmarked when they are considered obvious by native speakers or were introduced earlier for learners. E.g. كِتَاب (kitab) can be written as كِتاب.
2. Some diacritics are seldom used or even missing on Arabic keyboards, e.g. هٰذَا (hāḏā , “this) with a dagger alif (a vertical stick). So, you may see in a vocalized text هَذا, which would be haḏā, an incorrect shortening for the lack of the diacritic (or unwillingness to use it).

Oh, by the way @gillux. I don't have issues with using English personal or city names in Arabic and problems with transliterations are exaggerated.

So "Tom" is written as توم in Arabic, or تُوم with a vocalisation and no final case ending is added to foreign names like this. It would produce "tūm" but Arabs recognise foreign names and pronounce them imitating the foreign pronunciation for known personal or geographical names (sometimes adjusting to the Arabic phonology). It depends on the speaker, of course and there may be multiple ways of saying foreign names or loanwords.

On JPDB, you can filter out example sentences? Or are you talking on this site here?

I mean the rest of the sentence typically teaches me something useful; it's just the out-of-place name that's jarring. "今井先生は教えている" is fully native and feels right; "スミス先生は教えている" feels off because it's injecting a non-Japanese character into the action for no useful reason. (And one whose name breaks the Japanese phonology to boot.)

On this site, it makes sense when it's a translation of a sentence where the characters are named natively to the original sentence. But I always like to see whichever characters are native to the sentence's original language.