Perhaps I need to clarify.
It totally needs to be about warfare, but not quality nor quantity. Most 4X games focus on either very advanced tech to overpower the enemy, or large numbers. Here, tactics are more important: where you send your ship matters more than their tech level or numbers. Sure, having more helps you cover more ground and helps you be at more places, but at the cost of concentration of forces. If you spread out, you can't effectively take over a well defended base and so on.
I'd like a game where the player always controls less than 100 ships, in fact, if it could be below 40, all the better. Most games assume a ridiculous ratio where the planet:ship ratio is something like 1:1 or 1:>1. I'm interested in 1:<1

You are right though, no science if possible (infrastructures hardly qualify as science imo). Trade can happen, but the game won't create fancy UIs for that. If players want to trade, they'll do so using in-game mechanics such as messaging one another, dropping resources on the opponent's planet, etc. Politics will be a byproduct, but nothing formal will hold: no contract, just words.

I can see why this is confusing, but there's been a lot of games like that, but they are generally in the serious games or simulation labels rather than mainstream games

Check out Starship Unlimited. It's an old game where you had 3 or 4 ships at the most. It could have benefit from a few more, but it's old and was pretty nice back in the day.

The name popped into my researches, I'll give it a try thanks! Most of my research revolves around retro-dos titles...

The biggest challenge is making sure stack strategies do not become dominant.

That's one of the things I'm also very concerned about, but basically, each species comes with its own set of rules and limitations, and I do not anticipate this to be as much of a problem as it could be otherwise. Not only are ships very pricy (especially in finite resources) and that they require to be supported (fuel, supplies, ordnance, etc) but they also have their own limitations. Overall, it will be hard to dominate, in fact, I don't anticipate a player without any opponent would even be able to easily capture the entire system, nor would he care to.

If you have too many ships around a planet, they would drain its resources faster than it can produce it, stranding them or requiring you to have a big supply fleet.

I actually have a race that behaves like that: it simply can't stay on a world for long, which implies most of its fleet is always spent towards colonizing new planets so that 'the resource flow' (winks at Dune's universe).

Instead of moving ships to specific tiles, give them missions like disrupt supply lines, sabotage communication satellites, etc.

The game will be pixel-based, not tile-based. As a result, it will be easy to micro-manage interceptions, etc. Thus, there is no need for abstraction. An intercept course will try to match the X,Y of the intercept target and will be triggered once both ships end up at the same coordinates, etc. This does allow each player to play the economic war by using speed as their advantage to override interceptions and intercept ships of their own (freighters).
In VGA Planets, a well-cloaked ship could come in undetected, capture or kill a few freighters (then the opposing force would bring ships of their own). By that time, the cloaked ship would be long gone and the its action had acted as a good decoy.
I think that game captured the essence of doing more with less; there were no mentions of 'intelligence' or 'covert ops' anywhere in the game, but because the mechanics and map system were so great, people started to develop these strategies.

Spreading out will be one of many viable strategies that I've identified as something that I want to support. Each species have a set of strategies that work well, and others that are suboptimal (sometimes your core strategy is hosed and you need to do something else). During each review of the product, I intend on making sure these strategies remain viable and still make sense. In fact, racial bonuses/special rules and ship designs are to reflect the strengths and weaknesses of these species, and in turn, make these strategies stand out as optimal. There will be options, but not all strategies will be equal. For example, I don't anticipate player A and B to employ the same strategy to the same level of efficiency as species won't be on par with that strategy. This will avoid stagnation in the game (very few players can actually turtle, and they aren't aggressive in the same way, which avoids stalemates).