What you have to understand is that most words Shakespeare "invents" (and it is sometimes difficult to say whether he "invents" them or they merely arise in this era of profound linguistic productivity, with his being the first attestation) are not neologisms in the stronger sense of being lexical items unrelated to any prior items in the lexicon (e.g., "quark" or "grok"). Most are the consequence of contemporaneously productive and easily comprehensible word-formation strategies.

When we use a derivational affix such as "-er" in "murderer" or "ruiner" we do not need this particular combination of the morphemes in question to be familiar to us for the usage to be comprehended. The nominal suffix communicates its meaning perfectly well in a new environment. So when Shakespeare invents "injurer", there is no unclarity at all, though nor is this a word familiar to contemporary Modern English.

Even less so is comprehension difficult, when noun adjuncts (which are grammatical in English without inflection or use of a preposition) are rendered as a single word, such as "watch-dogs" become in The Tempest. If I were to say I have an "entry way guard post watch dog chain ring", the English speaker has no difficulty with my usage. And nor is any difficulty increased by my declaring it an "entryway guardpost watchdog chainring". It's a merely orthographic distinction.

There are exceptions to the rule that, generally, Shakespeare's neologisms (or possible neologisms - again, we cannot be sure they are his invention) are easily comprehended. Shakespeare does not mean "Honorificabilitudinitatibus" to be comprehensible English. It's very much the point that it's absurd, inaccessible Euphuism.

A number of Shakespeare's plays portray tedious, mannered, courtly speech in a court context. Perhaps most of all, Love's Labour's Lost, from which "honorificabilitudinitatibus" derives, but probably more famously, via Polonius in Hamlet, as the latter is so frequently performed, and the prior so seldom. So Shakesepeare's own voice is only half the cause of some of his more ornate language. Though he is guilty of some Euphuism, to be sure, certain of his characters are masters (and sometimes butchers) of courtly rhetoric. And that is very much intended.

When he is portraying the language of persons not practising the art of courtly rhetoric and exposition, his neologisms are of a much more familiar sort. For the most part, as I say, the consequence of readily understood derivational affixes, back-formations and noun adjuncts.