Weird question. But due to not having proper sanitation did even royalty smell pretty bad? I don't know if this is true but I heard that some rooms in the palace of Versailles, spare rooms were used for defecation. Is that true?
Well it depends on where this royalty is from (what region/kingdom).
I will not speak for the whole of Europe, but I do know quite a bit on bathing in Hungary (also take note that when I refer to Hungary, I mean the medieval kingdom, i.e Greater Hungary). As you may know, Hungary has an abundance of thermal springs, and its bath culture has existed since the foundation of the kingdom. However, the first thermal baths were built around the time of Mathias Corvinas (~1450). Once the Turks invaded, they also brought their bathing culture, and the ruins of many Turkish baths can still be found in Hungary.
Now for the aristocracy: Hungarian aristocrats during the medieval era were prolific bathers, which can actually be derived from their behaviour during the Renaissance and the Enlightenment. While the nobles of other countries were wearing wigs to prevent headlice (due to poor hygiene), Hungarian nobles in general preferred to grow out their hair naturally. Take a look at some portraits of Hungarian nobles if you want to see this (there are some exceptions, such as nobles that allied themselves with the Austrians). Another example can be found in Miklós Wesselényi's journal, when he mentions that while staying in a castle in the Holy Roman Enmpire, he had to open all of the windows in his room to let out the stench, and thus his room was freezing. This again highlights the culture of hygiene in Hungary, although I admit, it is a few hundred years after the medieval era.
In conclusion, a Hungarian noble would actually smell quite rosy in the medieval ages. However, I did not address perfume, because I know very little of it, and I hope that someone else will help you out in that department. One of my sources is a very simple, yet descriptive account in English of some of the points that I have mentioned, but I refrained from including too many Hungarian language sources, because I doubt there are many people who will bother reading them.
http://www.eu2011.hu/land-healing-thermal-and-mineral-waters
Just to point this out, Versailles only gained relevance in the 17th century:
hunting lodge built there between 1623 and 1624. In the early 1630s he had architect Philibert Le Roy rebuild it in stone and brick and purchased the seigniory of Versailles.
Versailles was certainly the last major achievement of this great architect of the middle of the 17th century. After the Grand Divertissement of 1668, Louis XIV entrusted Le Vau, Chief Architect to the King since 1654, with the extension of the brick and stone palace of his father Louis XIII.
Since many people attribute phenomena that would more accurately be placed in the renaissance or later to the middle ages, you may want to clarify your question.