Since the HRE was mostly German, and especially after they lost most of Italy, and considering that Slavs haven't always been viewed in the most favourable light in Western Europe, were there any negative perceptions of Bohemia among the mostly German nobility within the HRE? And if there were, did this change at all after the Habsburgs absorbed the kingdom?
The Bohemian nobility were treated differently, yes. However, this treatment had nothing to do with their ethnicity, which was all but irrelevant, and everything to do with the unique religious and political privileges the Bohemian nobility earned over the centuries. The Bohemians, in fact, required that their king treat them differently, and led major rebellions roughly once a century for four hundred years to protect and expand their privileges. You're asking about other nobles, however.
A brief note before I go on: "Czech" and "German", as such, didn't yet exist as distinct, important cultural or ethnic markers until the 19th century. Germans themselves were (and still are, though very much less so) divided into several large linguistic and cultural subgroups.
More broadly, cultural and linguistic differences were relatively unimportant to the Holy Roman Empire's nobility. Their shared class and knowledge of Latin, French and/or German allowed them to communicate with ease, and they certainly had far more in common with one another than they did with most of their subjects. The most important difference, by far, was in fact religious—the Bohemian nobility was distinct in this way after the Hussite Wars, although the resolution of that conflict made the Utraquist Church into an accepted part of the Catholic Church, minimizing the importance of this distinction.
The Bohemian nobility took to the Reformation very readily, and roughly 90% of them were non-Catholic by the (Second) Defenestration of Prague. They vigorously defended their right to practice the new religion, which set them at odds with the Catholic Habsburgs and their Jesuit-backed re-Catholicization efforts. This same defense, naturally, earned them respect from the rest of the German nobility (which was, itself, majority Protestant before 1610).
After Ferdinand II decisively defeated the Bohemian rebels and their Winter King, the make-up of the Bohemian nobility (and, increasingly, its lower classes) became more German-speaking, subjugated to their prince, and entirely Catholic. By 1648, then, they were very similar to the nobility of the Southern half of the Empire by virtually ever barometer.