Can my Yamaha Star Bolt have worn out its spark plugs after only 3,000 miles?

It's a 4 yr old plug, age can matter It takes 5 min to pull, clean, gap(if it is not platinum) install. Or just go big and buy a spare.

It could have also got condensation in the tank from sitting. Put a qtr bottle of HEET in the tank.

No. Plugs don't wear out in 20,000. You may have fouled them or bad gas or wrong heat range.

I replaced a few in an air-cooled Honda after20,000, not worn nor fouled, but I like you had a problem, so I changed them. Turned out to be rusty tank and crud in carbs. I sandblasted the old ones, good as new. Keep as spares.

I doubt the plugs are bad.

If you know the history of the bike, then chances are the plugs are the correct grade. It's nothing to do with being aircooled or not; Old skool two-strokes used to foul/oil plugs when used around town, but every four-stroke bike I've ever owned going back to a 1978 GS1000 has never had problems with plugs. Four bangers don't burn oil and the only way they can foul is if you use gas with too much lead on a plug that's too cold for the engine. Generally four strokes get their plugs good and hot and it's not a problem otherwise. As your bike seems to get little use, I'm going with water-contaminated fuel or maybe some sediment/rust/dirt. Flush out the carbie floats and fill it up with fresh gas.

The term 'worn out' is not quite accurate, but they could be in need of replacement. The truth is that motorcycle ignitions are crap by automotive standards. Plugs in cars can last 100k miles, it's because they are connected to an energetic ignition system that can still easily push a spark across huge gaps across electrodes rounded over by 10's of thousands of miles. Motorcycle ignitions are so anemic that they struggle with much smaller gaps, and need plugs with relatively crisp edges to help that little wispy spark make the jump. There are no motorcycles with 100k mile spark plug replacement schedules, most come no where near what cars have.

If you run E-fuel and the bike sat for a period of time than the fuel is sh!t. The E starts to turn itself back into corn where it came from.

Ah... the random replacement method rides again... and I love your premise that all new plugs are perfect... but it's a relatively cheap fix, and if it doesn't work you can save 'em for later. I would be more inclined to drain the tank through a clean cloth to see what's in the gas, blow out the fuel lines, pull and clean the finger strainers and maybe add aftermarket fuel filters.