If shielding from cosmic radiation is important, big ships are more efficient.
One of the major challenges for crewed interplanetary spaceflight is the health risk presented by cosmic radiation. This is a big problem even for a 180-day journey to Mars, let alone a multi-generation trip between stars.
The linked Wiki article mentions an indicative figure of about 4 tons shielding per square metre to bring radiation levels on a space station down to roughly earthlike levels. There's a fair bit of uncertainty on that, and requirements for interstellar travel would be different again, but it gives us a ballpark: if you don't have some other way to protect against cosmic radiation, physical shielding is going to be a big part of the weight of your ship.
It's possible to have shielding that's also useful for other purposes, e.g. store the ship's water supply or hydrogen fuel in its skin. But for a generation ship, you probably want near-100% recycling of resources, meaning that the amount of water you'd otherwise need to carry is likely far less than the amount you'd need for shielding. Even if you're using consumables for shielding, you still need enough left over at the end of the trip that you're adequately shielded in the last years, which still means a large increase in the amount you have to carry.
If the weight of shielding is a major design constraint, then your ships are going to look like big balls, because that's the most efficient shape in terms of surface area per volume contained. (Edit: As mentioned in comments, some components can be put outside the shielding, so more like "big balls with stuff hanging off them"). Thanks to the square-cube law, one 200-metre-diameter ship will hold as much payload as eight 100-metre ships of similar shape, but with only half the surface area and hence half the weight of shielding.
(In fact, the big ship requires a bit less than half the shielding of eight small ships, because thickness of shielding is likely to be non-negligible, but let's not worry too much about that.)
So, if you're dependent on physical shielding for radiation protection, and you don't have some super-light unobtainium shielding, you probably want to go with a small number of big ships.
Another option might be magnetic shielding. This is a bit more speculative, but the requirements for that will probably still scale roughly with the surface area to be protected, which again makes bigger more efficient.