Capacity will be increased by the increased frequency on the core, correct, and it will be interesting to see how much demand materialises for the reopened line and the extensions.
I agree however that having only 4 car trains could be problematic if demand increases significantly. The major constraint is of course the length of some of the platforms on the original ELL and the difficulty and expense of extending some of these.
Most of the platforms, with a little refurbishment of disused parts, can take 5 cars without too much trouble, some would even take 6 cars. The worst problem though is Canada Water, which is 4 cars and no more. The ELL was closed when this was built, and possibly would need to be again for a significant period if it were to be extended.
One option might to insert another carriage to make 5 car trains and use SDO at Canada Water - this is what's been done on the DLR at Cutty Sark to allow 3 unit operation. Given the walk-through nature of the Class 378 this shouldn't be a major problem, and it's likely the same will be done at many stations on the Circle line when S Stock comes into service.
Another possible option would be a few 6 car trains as through services from the south stopping at only New Cross Gate, Shadwell and Whitechapel on the original ELL, but that makes it a more complicated service to operate and regulate, losing the commonality of the fleet.