I don’t know if Israel counts as a “top country” in this regard, but it does have a problem with transliteration of Hebrew into English (or in Roman characters in general).
Essentially, the problem is one of what is known in information theory as information loss: in the process of converting from Hebrew to English, information about the spelling of words (including the distinctions between letters that are essentially homophonic, such as ḥet and khaf, tet and tav, kaf and quf, samekh and sin, etc.) is lost, so if you were to try and convert back to Hebrew, you wouldn’t be able to reconstitute the original spelling—even if you were a native Hebrew speaker and recognised the words, as in the following example, from a poem of homophones titled:
The following is a poem to illustrate how the spelling distinctions between homophones in modern Hebrew are irretrievably lost in the conventional phonetic transliteration of Hebrew in Roman characters (when necessary):
If you ever wondered why the Russian letter sha (ш) is so similar to the Hebrew letter shin (ש) (which, to be frank, you probably haven’t, unless you’re a Russian-speaking Israeli), the reason is, of course, that the Cyrillic alphabet is derived from the Greek one, which in turn was derived from the Phoenician alphabet, which was also the original Hebrew alphabet, in which the shin was a w-like character:
True ligatures, in the sense of a character made up of two enjoined letters, like œ or ﬂ, don’t really exist in Hebrew—with the possible exception of the double yod (ײַ), which was common in Yiddish, but little used in Hebrew (most people aren’t even aware that has its own keystroke).
If you mean instances of joined-up letters in modern Hebrew cursive (as I suspect you do), those are mostly precluded by the very nature of that cursive.