A ship that doesn't wait means that he has to continuously browse the job list. That will be very bad for performance.
LU's main performance gain comes from the new rate of fire (i.e. if you increase it back to its vanilla value, you'll instantly feel the difference - other changes are important as well of course, but more subtle). More improvements could maybe made by reviewing all scripts (especially ones that are assigned to job ships), but I'm sure the real problems are hardcoded (new rate of fire fixes a symptom, not a cause). The scripting language is slow, and I know that it can be improved. But not by me
I didn't make any serious performance tests with the new DAs. I'm pretty sure they're fine as they are; but not if you force them to search a goal every millisecond...
X3 has too many ships. It would be better to make each of them a bit more important, by creating new systems, rather than increasing their number.
On a side note, I'm under the vague/abstract/mystical impression than 3.3 did some good to performance... Maybe it's just me...