[RPG] When a wizard copies a new spell into his spellbook, it costs 50 gp. Where does that money go

This makes it sounds like a wizard would have a really hard time to prepare a spell from another's spellbook. Is that the case?

That is correct.

As you quoted, each wizard's spellbook notation is unique, therefore you can't prepare spells from someone else's book.

You must first copy the spell into your own book (deciphering the notation in the process), after which you can prepare it as normal.

Your ruling is unlikely to break anything. However, the rules on their own (and the underlying fictional significance of the rules) appear to answer this with a No.

The surface rules difficulty is that a there's no object duplication involved — you start with a spell scroll and end with a page in a spellbook. These aren't identical objects, as the ability requires.

One might argue that they are the same, just with one bound into a book and one not, but spell scrolls and spellbook pages aren't functionally interchangeable either. They function differently and contain different information: you can cast a spell off a scroll, thereby destroying it, but you can't cast a spell off a page in a spellbook in the same way (and if you do it as a ritual it works differently, and doesn't destroy it); similarly, understanding the scroll is harder than understanding the page in the spellbook. The two objects are distinctly different and the kenku's particular skill doesn't come into play.

But this mere rules difference reflects a deeper meaning: how learning spells from scrolls works in the fiction. The normal process of “copying” a spell from a scroll into a wizard's spellbook actually involves a translation: from how the scroll presents a ready-to-cast spell, into a record of the wizard's own personal understanding of the nature and process of preparing and casting the spell. The Arcana check for copying appears to represent the possibility of failing to extract the necessary understanding of the spell from the scroll's not-a-spellbook formulation, and thus the possibility of being unable to scribe the spell due to simply failing to actually learn it from the scroll. Being good at duplicating things doesn't help with learning arcane secrets of the universe.