Note that neither library is binary compatible to its predecessors.
libEBML changes include several new API functions like GetValue()/SetValue(), new constructors, and a couple of bug fixes like calculating dates with 64bit integers preventing overflows in certain situations.
libMatroska has received several new elements that were added to the Matroska specifications: CueDuration, CueRelativePosition, ChapterStringUID, VideoAlphaMode and DefaultDecodedFieldDuration.
For both packages the build files for Debian packages have been removed (the whole "debian" sub-directory). They were out of date and Debian-based distributions already provide their own versions of the files in question.