The Lookup References command has a few options that affect its speed.
The Smart Reference Matching option means that the search is context-sensitive; the search results will only contain matches for references to the exact symbol you specify, using the surrounding context. This option slows the process down because each same-string occurrence has to be qualified with a symbol lookup, which requires some parsing on the fly. If you turn this off, it will work like version 2.x of Source Insight.
The Skip Comments and Search Only Comments options also slow the search down a little, but not as much as the smart reference matching option.
The Smart Rename command also uses these same mechanisms.