In general, people who remap don't get much better fuel economy. In fact, some get worse, because they tend to use the power that is there, rather than trundling along. You don't get something for nothing. Extra BHP = extra fuel used.

The downsides of remaps ? The old owner wanted more power (say that in a Clarkson-ish voice), so how do you think they generally drove it ? Like granny coming home from church, or like a rep running late ? That MIGHT translate into more wear and tear on the engine, turbo, gearbox, suspension, etc. Also, generally on 'chipped' cars the chip means that the turbo is running more, so possibly a shortened turbo lifespan there too.

Regarding the clutch ... well, diesels have dual mass flywheels (DMFs) because they have lots of torque at low revs. The DMF acts alongside the clutch to reduce torque shock on the gearbox, otherwise the wear and tear on the gearbox can be quite substantial. But, a 'chipped' car has more BHP, and (usually) more torque, so is likely to go through DMFs and/or clutches quicker. And those aren't cheap.

Also, insurance. If you tell them it's been chipped, then they might just charge you extra. If you don't, and if you have an accident, then they might not cover you, or reduce your cover, due to modifications.

So all in all, is a 'chipped' car worth more ? I wouldn't pay more for one. In fact, it's less attractive at the same price, in my opinion, due to the reasons above.