Right then,
The 110 has got rear discs with an inner handbrake drum set up and these can give trouble by siezing etc but regular inspection/cleaning/copper slip where needed will prevent this. The 90 has rear drums only so simpler.
The 110 has got a dual mass flywheel which can wear and cause slippage/vibration this is a £600.00 job. My DMF is worn but then again it's been like it for 2 years, very occasionally slips but doesn't make the driving a problem. The 90 just has a solid flywheel.
The 110 adds an intercooler which could corrode and leak although very rare.
The 110 has more complex fuelling and turbo control over the 90 but rarely gives trouble.
The 90 is reported as being sluggish which will get on your nerves. The 110 is quite fast as standard.
If it was me - if I found a minter of a 90 with good history etc I would snap it up and get it chipped to 120BHP then you would have a simpler motor with decent power. That is what I would look to do although I don't think you can get the 'exec' in 90BHP guise if that's what you wanted.
Don't be put off by a 110 though especially one that's come off a fleet with loads of history and had a new clutch fitted
One thing to note is that the last of the HDi's 03/04's had more complex emission controls which will see you down at the dealers a fair bit with 'errors'.
Hope this helps.