Yes, ship building and the ships themselves affect your income in two ways:

1.) When you build ships, your income will decrease since you are spending money to produce manufacturing points that will build up towards a shiny new ship (ie, the cost of the ship is in manufacturing points). If you are strapped for cash, halting production on some planets is a good way to tighten the budget.

2.) Ships with weapons and constructor modules will cost you money in terms of upkeep every turn, which is about 3% of the original cost of the ship. If you need money fast, selling off ships or disbanding them maybe a way, although it is not usually recommended (especially for veteran ships) except as a last resort.