The size of any ship is going to be dictated by a multitude of factors. Having multiple hulls for redundancy is certain one of them, but only one. After all there's a reason the US built eight 40,000 ton Wasp Class
amphibious transports that can carry 1800 troops each, rather than eight hundred 400 ton ships that can carry 18 troops each. One big ship can bring capabilities that many small ones lack - try operating an AV-8B or F-35 off one of those 400 tonners, or mounting decent radars and SAMs on them.
And bear in mind the potential scale of a sci-fi military operation. If the Dominion had wanted to invade and occupy Earth, how many troops would it take to control a 9 billion population? I did some googling to try and get a handle on the sort of numbers you might need. Police forces run about 1 cop for every 450 people in the UK, matching that for 9 billion people would require twenty million troops - and police forces are only really able to govern because the majority cooperate with them. Meanwhile there are half a million troops in Afghanistan, to control a population of thirty million, and it's not exactly the most stable situation in the world. On that scale you would need to land no less than 150,000,000 troops on Earth even to have partial control over it.
If you imagine a war where a thousand planets are fighting, then you're going to need to move armies around in the tens of billions, at least. So yeah, some pretty big ships might well come in handy.
What often annoys me about big ships is that people don't get the "rule of cube". People make ships miles long and basically treat them as if they are dinky little things. But if you scaled an Arleigh Burke class destroyer up to 1 mile long, say, it should have a crew of around 300,000 people and carry upwards of 95,000 missiles (or the same number of missiles but a thousand times the size...) Running it would be like being the mayor of a city.
The only time I ever saw anything in sci fi that resembled how big ships should be treated was the way command of Babylon 5 was dealt with.
Give a man a fire, and you keep him warm for a day. SET a man on fire, and you will keep him warm for the rest of his life...