Wartime expences can be devastating, no doubt about that. There are things you can do to counter each of your concerns.
1>* maintenance on ships getting high as my fleet gets big 2>* loss of taxes as population gets put on invasion transports 3>* sudden added cost of colony maintenance when I conquer planets
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1> Watch out for excessive defenders. During peace time, of course you want some ships orbiting, as the bump you get in attack value can avert a war (until your ready). IMO a good design for this purpose is your fodder ships. These are weapon only stat boosters that have the same speed as the capital ships. I like the tiny hull for this purpose. Enough room for 2 engines and enough weapons to keep it on the front line when you fleet them. Added bonus is they are easily replaced by the planet your pulling them off of. If you can, make them slightly more expensive than your primary constructor design (war time switch-overs made easy effective).
2> Plan you wars. I make two transport designs. One is a tiny hull hopper (1 adv trp, rest engines) and one 3-4k carrier. Use these together when invading. Prior to starting a war, make sure you have at least half of the ships you will need already built, filled, and NOT in orbit (OWP: off world population). This is so your initial thrust does not decimate your empire population.
2b> Of course this tactic assumes you have paid attention to your approval rating. (I dissent, 2 VRCs per farm is a minimum, 3 if the farm is on a bonus.) Any continued problems with morale can be dealt with using carriers. The extra VRC allows much better growth and taxes.
3> In conjunction with 2b, this will have minimal impact, as you re-plan the lay of the land on your new planets.
If your economy is still suffering after your initial military production switches, as the minor producers complete their constructor/fodder, shut down military and switch to tech. Even if your going from 80MP to 5RP. Spread that drop out amongst a number of planets and the savings add up. With the industrial capacity slider being your guide, manage the increases back to 100% capacity as your able to shut down the minors. Shutting down a major MP producer can provide additional cusion while you deal with the minors. The other reason for MP shut down is ANYTHING on the SP build list.