The "hull size" limitation for a warp point defines the maximum hull size of a single ship which can make transit through it. This does not mean that only a single ship of the specified size can make transit simultaneously; only that no individual vessel larger than that can use the warp point. And there are some warp points which are small enough that only a battleship or smaller can squeak through them.
The actual total volume of a warp point is on the order of about 50-60 kilometers. However, there are 3 factors which make that area smaller than it might seem:
(1) A warp point is not a sphere; it is a hemisphere at the moment of transit. (That is, when entering a warp point, it "manifests," if you will, as a spherical volume regardless of your approach vector. But when exiting a warp point, the ship in transit crosses a plane which bisects the sphere and leaves it only a hemispherical volume into which to emerge. For those who play the game, this may not be obvious from watching it on the map sheet, but remember that you are dealing with an essentially two-dimensional representation of a three-dimensional problem.)
(2) Time does Strange Things during a warp transit. As far as anyone can determine, transits are instantaneous; in fact, they are not, and ships can actually "pass" one another in transit if they try to pass through a warp point in too tight a sequence.
(3) The nature of the transit itself is such as to "squeeze" a transiting ship (or ships) down into a narrow "neck" just before they reenter normal space. This compresses the volume of normal space available to them even further and, combined with the Strange Things that happen to time, greatly increases the chance of two or more ships to reemerge into overlapping areas of n-space, at which point Very Bad Things happen.
I should also point out, that this problem applies only to vessels (including missile pods) making transit in the same direction at the same time. The problem is overlapping on emergence from the warp point, and, obviously, ships going in opposite directions are going to emerge on opposite sides of the warp point, where they cannot be occupying the same volume of space. Should a ship try to emerge into a volume of space already occupied by a ship which is not simultaneously coming through a warp transit, the result will be a collision, not an overlapping situation. (Note: Assuming that both ships are moving a .1 cee when they collide, the practical consequences of the difference will probably be nil, of course.)