New update 0.8.9ubuntu2 fixes this bug.
I do not know if the properties that caused this bug (enable of compressed
indexes) was withdrawn.
Perhaps Martin Pitt can comment on this.
** Changed in: apt (Ubuntu)
Status: In Progress => Fix Released
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[Natty] apt_0.8.8ubuntu3 seriously slows down synaptic
https://bugs.launchpad.net/bugs/675641
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