Yes, athwartship doubles can require the person on the inside to have to crawl over the person on the outside - although for couples who still enjoy some physical contact, this can actually be a nice start to the day! Unless they are 'island berths' (which in cats of 40 feet or under LOA
requires pretty excessive beam aft), fore/aft berths still require someone to crawl out of a tunnel and in my experience this is still apt to awaken someone sharing the berth.
In terms of motion while underway, I am with those who say depending upon the conditions/point of sail, there is very little difference. Unless a boat suffers from excessive hobby-horsing, when reaching there tends to be more motion side to side which favors athwartship berths; when sailing to windward (or downwind in large waves), a fore/aft orientation is typically more comfortable.
Another issue which can have a dramatic effect on comfort, however, is the how the bridgedeck and tunnel were designed in order to accomodate these berths. Some cats with large athwarthsip, forward doubles have a flat bottom and a very blunt leading edge to the bridgedeck: this will increase pounding generally, but also specifically underneath these berths! Other boats accomodate berths over large 'shelves' that protrude into the tunnel. These can reduce bridgedeck clearance under the berths to a matter of inches, again contributing to pounding underneath the berth when underway.
As to noise
from the diesels in aft berths when underway - I see this as a pretty rare occurence. On longer passages, you will typically be using the engines primarily when entering or exiting harbours - and at these points, you will usually want your crew to be awake! If becalmed and in a hurry, unless in extreme conditions we usually motor on only one engine
and can choose to use the engine
in the opposite hull of the aft cabin that may be in use. We have a fore-aft berth forward in one of our hulls and I can say that noise
from waves while underway is tyically greater there than in the athwartship aft doubles.