You're not talking about a real explosion with shrapnel flying. It's just a wasted bottle. I've broke tons of canning jars in boiling water and some of my antique ones are full of bubbles, who knows how many boiling water baths they've seen. I use dry heat in the oven to sterilize my beer bottles at great risk to losing bottles, but I've never lost a single one (and some have a lot of air bubbles besides not being rated for dry heat sterilization).
If a piece of glass would go flying it would be small and not likely to have enough momentum to carry through the resistance of water. Just don't take a facial steam bath while you boil and you should be safe.
The above suggestions to drop them in boiled water will waste more bottles from thermal shock. Best to set them in water before it's boiled, bring it to a boil and then let it cool some before removing. Thermal shock is where I lose most of my canning jars and they're hot packed so they should be hot enough there's not much shock.
In my experience heating glass that's not supposed to be heated, be careful of thermal shock and you'll have good results. Heating glass that is supposed to be heated and ignore thermal shock and your results will suck.
That said, so far I haven't worried about it with eliquid. I don't see where the risk is.
Even with my high VG I don't think VG "going bad" is related to contamination but oxidation/degradation. If people are leaving the caps off bottles for days to steep the risk is not high. Try leaving the cap off a canned food item for days.
If I was to worry about it I'd use dry heat in an oven because my water is too hard and would drastically lower the pH from the hard water deposits left inside the bottles after boiling. Or I'd use Star San, just because I always have a jug of it around (note that Star San is sanitation not sterilization like heat is).
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