Sounds like it will be quite complex, indeed. While I wouldn't say that Construct wouldn't be able to handle the data storage and manipulation with it's native data structures, I would suggest thinking about using lucid's 's' plugin, or Python Classes, to deal with all of the data needed for such a game.
I have not tried the 's' plugin. It sounds like it would fit the ticket nicely, though. Since I am quite comfortable with Python, though, I would definitely use classes for each of the components involved. Object-oriented strategy would work well for something like this. At least, one can use Python Classes as a sort of c-like 'struct' in which one can have structured groups of different types of data with meaningful names. These are also capable of pointing to each other, thus 'linking' to each other. It can be a bit tricky interfacing Python code with Construct's events, but it's not too bad...
I'm not sure of your sectioning of the game universe, but off of the top of my head, I can see I'd want some basic data structures like so:
Ship:
- 'Health'
- Speed
- Armor
- Class of ship
- Armaments (list)
- fuel capacity
- current fuel
- cargo capacity
- current cargo (list)
- current location
Station/Planet:
- sector located in (link to sector)
- Type of economy
- population
- crime level
- needed goods (list)
- surplus goods (list)
... etc
Sector:
- bordering sectors (list of links to other sectors)
- ships in sector (list of links to ships)
... etc
... and much more data than that, depending upon the complexity desired. The trick is to make it as simple as possible in the hidden inner workings of the game, while making it seem complex/realistic to the player. It could be as simple as having an array/list of ships that you loop through every tick of the game, having them make decisions based upon semi-random choices.