Usually Wizards need to use high quality ink and paper to copy spells into their spellbook. Deciphering a Spellscroll takes an Arcana Check as you described, but the material components to copy the spell are still required.
"Copying that spell into your spellbook involves reproducing the basic form of the spell, then deciphering the unique system of notation used by the wizard who wrote it. You must practice the spell until you understand the sounds or gestures required, then transcribe it into your spellbook using your own notation.
For each level of the spell, the process takes 2 hours and costs 50 gp. The cost represents material components you expend as you experiment with the spell to master it, as well as the fine inks you need to record it. Once you have spent this time and money, you can prepare the spell just like your other spells."
The gold cost is simply streamlined in the game, because otherwise you would constantly be on the lookout for someone selling paper and ink. At least that's what I would assume.
