If another empire has way more colonies and produces ships like crazy in late game, here's how to beat it:

Hopefully you still are at peace with them.
Build battleships with Battle Pods and 1 Stellar Converter plus whatever rudimentary defense systems you may be able to squeeze in there. Or build Doom Stars with 3 Stellar Converters on separate banks. Group a few of these, say 4-5 battleships or just 1 Doom star plus couple of battleships. and send them around the galaxy in strategic positions (near enemy colonies, obviously). Maybe leave some in reserve, but don't spread out this reserve: Use it to guard your most important star system, IE somewhere heavily fortified, with multiple planets pers system.

When the fleets are in position, send them out as small battlegroups as described above. 3 stellar converter shots per turn from your fleet should be able to neutralize the defenses of a star system if there's no fleet, a Star Fortress and all of the ground defense buildings are no match for stellar converters if you get to shoot first.

Hopefully you spread out the fleets in a way that multiple enemy colonies get attacked per turn. If you absolutely want to cheese out this approach, you can even destroy the enemy planets with the stellar converter afterwards, thus limiting their potential re-colonization efforts after your fleets leave. At some point when enough enemy colonies have been destroyed, you can re-group the smaller battle groups into a humungous fleet, because the AI seems to love attacking with huge fleets. This way, you may be able to experience a huge battle before your fleets turn all enemy systems to gigantic asteroid field graveyards.

This approach takes advantage of the AIs ineffectiveness to counter attacks on multiple systems at the same time and preference to create a single megastack of a fleet at late game, but it isn't cowardly. The late game wars between strong empires able to field multiple dozens of ships are always going to be destructive and there's not as many single decisive battles as say early on if you manage to annihilate the whole enemy fleet and then grab quickly multiple colonies from them. So why not limit your casualties?