Egg modification doesn't affect worldgen in any way, and same goes for LITTERSIZE tag. Worldgen creatures seem to be unable to have more than one kid per year.
The main problem kobolds have, I assume, is food. Yeah, believe it or not, but DF has some basic simulation of this for civs. INDOOR_FARMING, OUTDOOR_FARMING, INDOOR_GARDENS, OUTDOOR_GARDENS, INDOOR_ORCHARDS, OUTDOOR_ORCHARDS are the tags that should help straight away - pick any combination of those or all at once, whatever you prefer. RIVER_PRODUCTS and OCEAN_PRODUCTS also help, but only if the civ has sites near a river or an ocean respectively. Vanilla kobolds have none of these tags, presumably to show that they are hunter-gatherers and, thus, can only live in small tribes.
Source: once I was fooling around wih variable human civs and my nomadic horde style guys performed very poorly in terms of population, until I've given them farming, fishing and encouraged them to settle along the rivers. All of these changes were done one by one and each had a noticeable effect on pop number.
I don't think you even need to change the site type for this to work, but I don't know for sure, so, try out and see for yourself. One thing I
can say for sure is that when a cave is conquered by a successful human/goblin/elven civ, it can sometimes reach a population of more than a thousand.
You can even embark on such caves.