I'd go ahead and propose that no, it does not matter.
Technology and environment.
Mickey in a comment and M-i-ech also indicated: it really depends on the technological level.
But generally, we will have to accept that the technology of space travel has develop well enough to have actual ground to start a way. So sending space shuttles to the other planet would not be too difficult for either.
From that we could suppose that they have some space stations orbiting their own planets, or based on natural satellites, or even relatively closed planets. So we don't talk about two planets at war, but two planetary systems.
Distance and orbits.
The two planets orbit the same star. This is a problem for your military tacticians. You need to spend quite sometime calculating precisely the trajectory for your ballistic missile to reach a valid target on the other planet. And that is including your respective revolutions.
If the planets are too far from each other, that's going to be a real pain. And sending your ICBM from another place might be more useful.
If, on the other hand, they are too closed, they will end up orbiting one another.
You should also note that the further you are, the more the other guys can anticipate your missile re-calculate the trajectory and possible aims.
Costs analysis
So both use the same resources to build the missiles ($M$), but the LimaPorters, the inhabitants of the Large Planet have to place more fuel or slightly smaller missiles. Note that the escape velocity is $v\propto\sqrt{m_p}$. To simplify, we will write the total cost for the missile as
$$C=M+L\sqrt{m_P}$$
Your theory was then to say that it's easier for the smaller planet to send those missiles and thus they'd gain an advantage. However, all else being equal, they also dispose of less resources. We have $M\propto R^3$, the radius of the planet. So the cost, in proportion to the natural resources (modelled by the surface) becomes
$$\frac{C}{S} = \frac{M+L\sqrt{m_p}}{S}\propto\frac{M+L\sqrt{m_P}}{R^2}\propto\frac{M+L(m_p^{1/2})}{m_p^{2/3}}$$
which strongly reduces the advantage of the smaller planet. Furthermore, with the same charge, the same precision, they'll hit the same number of people. Which, due to the same density, will be much more damaging for the smaller planet.
Thus, while the absolute cost is much higher for a much larger planet, and the absolute effect is the same, the relative cost is actually smaller and the relative effect is much stronger.
Likely warfare
With the given technology and environment, it is very likely that they'd launch their missiles from a moving base (spaceships) as they would provide a more flexible and tactical advantage, comparing to launching from your ground.