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I don't know if it is hierarchical tags so much as just tags. At least I remember another post saying that populating the Tag Browser on loading a Library is the primary reason for the delay.
When performing searches, the delay is because of the number of records by the wide variety of fields/columns to be examined for a generic search. There is a way to limit the fields a search will check, within Preferences>Look and Feel, I believe.
As for Edit Metadata... I'm not sure what might be responsible other than the overhead involved in updating two files. Each book would be altering the metadata.db for the library and the individual OPF file save per book.
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