I must admit if I'd been told straight up that a battery had been deep discharged for 30 hrs or so, I would probably replace it, though I suppose if I then attended the system some hours since the power was restored, and my ACT tester was showing 7ah (I.e OK) I possibly wouldn't rush to replace it..
Also if I turned up to any job and was told it hadn't been serviced in years, I too would assume this meant all batteries were ancient nd would offer to replace them as a matter of course.
However, I have now just re-read your post and didn't realise the system was only 21 months old (I'd still recommend device battery changes though, Scantronic suggests 3 year life absolute max. for most devices...) nor that you'd invited back the original installer.
Bit of a funny one, price not really outrageous if I'm honest, possibly a slightly odd approach re. Device batteries, and yes, I would pass invoice to builders esp. If NOT itemised!
Unfortunately not a very good system in the first place, and I assume your previous systems were not wireless and *should* have been regularly serviced.