Larger guns were generally better, both in terms of penetration and range. The fact that the larger guns in the game appear to be more accurate may be a product of the fact that accuracy appears to be a function of range to target versus maximum firing range, thus larger caliber guns that have very large maximum ranges are getting better accuracy at typical engagement ranges.
I also think the historical balancing factors for huge caliber guns - weight of the guns turrets and mounts and also production time and cost - aren't really relevant to the game as it is now. I imagine that cost in particular may well be a factor when we get the campaign because trying to have a fleet with 10 x Yamatos should be prohibitively expensive.
All that being said, it'd be nice if some of the guns are 'anomalously' accurate e.g. the British BL-15/42 and the US 16/50 caliber.