Is it cost-effective to upgrade an old-ish Giant Escape R3 commuter bike with entry-level branded parts (wheels, drivetrain)?
Cable replacements, chain, tubes, all those are "consumables"  Even spoke replacement is not an uncommon problem to have periodically.   A bike isn't a cellphone to be discarded when its a bit tired - periodic maintenance is easy.

Consider that if you were using a car, there would be oil/filter changes and fuel, perhaps a light bulb every couple years and a windscreen once a decade, plus whatever checks and tests your country requires to licence vehicles.  These are all "the cost of using the tool" over time.

Now - your specific points:



Latex tubes will be flat every morning - they're not good at retaining air.  But they're lighter than Butyl rubber so good for racing.

I've never heard of latex/butyl hybrid tubes.  Could be you're thinking about butyl tubes with liquid latex sealant inside them, ready to seal up holes as soon as they happen.   These are heavier again than plain tubes, but can help if you puncture.

Also you can't patch latex tubes - one puncture and they're useless.



Generally speaking, the cost of upgrading components is much higher over time.  If your existing component is worn out (say the rear derailleur was busted) then the cost of a like-for-like replacement is the sunk cost, and the difference to a higher spec one is the opportunity cost, or the "cost of upgrade"  which is the perfect time to do so.



The common wisdom is first you need to be comfortable on your bike.  That means you have the saddle and bars and ergonomics sorted out to suit yourself.

Once that's done, tyres (tires) are the first best upgrade, followed by the whole wheelset.  You probably don't want to splurge on top-shelf wheels like Zip, the benefits over mid-range product are marginal, and you'll never be able to leave your fancy bike locked up alone, ever.

Schwalbe Marathon anything tyres are puncture-resistant commuter tyres, which is fine.  If your goal is to go fast then race-oriented tyres like Continental GP series would be faster and lighter, but at an increased risk of punctures.  Check out http://www.bicyclerollingresistance.com/ for many comparisons there.



As for crankset/BB - I'd only change if the chainrings are worn, or the BB bearings are not smooth.  Your existing BB cartridge should spin smoothly with no play, so only replace it if there's a problem.  $19 for a replacement cartridge unit is cheap, but that shimano one should be good for 5,000-25,000 km depending on weather.



The single best upgrade for a commuter bike is... Fenders (aka mudguards).  If you ride in the rain, then life is so much nicer when you get there cleaner.