Well, you *DO* want the nuclear reactors away from people...
A reason to keep the three reactors in three separate hulls – and separated from the saucer hull – is to protect the people who reside inside the saucer hull in the case of an emergency. For example, if a meteor strikes one of the reactors, the reactor can be jettisoned away. This is a case where the Enterprise ship basic configuration that has been lifted from science fiction fits nicely with the functional needs of the actual Gen1 ship design.
Another reason to have the three reactors in three hulls set away from the saucer hull is to reduce the exposure to any low level radiation from the reactors on the people and electronic equipment in the saucer hull. While the reactors will be heavily shielded to block the release of radiation, some gamma radiation and neutron radiation will still escape at a low level. So “distance attenuation” is a strategy used to further reduce this radiation. Distance attenuation takes advantage of the fact that radiation from the reactors falls off by the inverse-square law. While short term exposure will cause no ill effects on a person’s health, such as when workers or visitors are in the main engine hull or aux engines hulls, long term exposure might pose a health risk. Thus the reactors are located at least 250 feet away from the saucer hull at all points.
I kind of felt the same way the E did looking over the site (and I wasn't too happy about it, I
want the design to be viable); however, the author does make some points for his design that aren't discernible with just a casual glance at the website. However, I wish he'd spent some time, you know, actually covering a few bases like
1) How he plans to get all of his stuff up there (this may be possible but not right exactly now, we need some sort of heavy lifter, and it needs to be efficient or the cost is going to be nutso) and
2) how he plans to get these fuel depots in place and fueled -- ok, good, now how about
re-fuelling them?? Yes, the Enterprise will
use that fuel and need more.. you'd need another fleet of fueling ships (that doesn't make this impossible, it just means you need some infrastructure in place is all) and
3) How is this thing going to break orbit with .002 of constant acceleration.. is the plan just to increase speed slowly and go into increasingly wide orbits of the Earth until escape velocity is reached?
EDIT: The only thing I don't like about having the gravity wheel in front like a big shield is that it makes a nice big meteor target... maybe if you put it up on its side, and had four small reactor / engine pods spread out at equal distances from it, then it wouldn't have any problems spinning the hull around (ok, actually it might spin, I see that now but this could be countered by having ion compensation thrusters maybe... IDK - I just don't like the idea of plowing through space with a nice, big flat surface that happens to be the habitat ring in front)
Like this:
^ direction of travel ^
ll
engine / reactor pod > |--ll--| < engine / reactor pod
ll
^ gravity wheel
view from top ^
__ <engine / reactor pod
_|__
/ \
| | <gravity wheel > Direction of travel
\ /
-----
|
---- <engine / reactor pod
view from side ^
This would make for a smaller profile to avoid meteorites / space dust (assuming high relativistic speeds were ever reached)
Right?