Please remember that the current population numbers are (I think) placeholders for economy system balancing; Alex or David said something to that effect somewhere, I'm pretty sure. It is not unreasonable to expect that the core worlds could have billions of population, which would allow the major factions to garrison their less populous planets with lots of soldiers. The pirate bases even might be a bit under-populated, given that pirates can be seen operating cruisers when even a Falcon requires 100 crew.
To use a real life example, the USA has a population of ~320 million. ~1.35 million of those people are active soldiers in the military. That's about 0.4% of the population, which is high compared to many other countries. If we say that the Hegemony has only 1 billion citizens and maintains 1% of its population in its active military (given the dangerousness of the Sector), then that's 10 million soldiers, or about 3 to 10 hundred divisions (10 million is enough to crew 20,000 Onslaughts, to put it in game terms). 50 Valkyries (100 Logistics points, not counting crew/marine costs) can only carry 14,500 marines (+500 crew).
In respect to the argument that ships are worth more than marines (I'm assuming specifically regarding attacking a station/planet), I say when given the shield systems ships are able to mount, presumably stations and planets with their huge power grids would be even harder to crack. It could be like castles or fortified town before cannons: the most reliable way to capture a fortified position is by besieging it until they surrender.
Although, when it comes to actually assaulting a station/planet, Alex and co. could take it a number of ways. Perhaps there's some kind of phase shuttle that can be used to bypass the massive shields of stations and planets. Perhaps shield domes over planetary bases can't block troops on the ground effectively (shields have problems with solid objects, like, say, the irregular and very solid surface of the planet). Perhaps, even, you actually have to blast through the shields before you can start landing troops to capture the infrastructure. I am sure there are many, many more ideas, ways, things, and so on that I haven't even considered.
with a human attack fleet of 5 onslaughts, the Crystantite population was nearly destroyed.
That is from either fanfiction or mod lore, but definitely not canon Starsector.