We have travelled between Ibiza, mainland europe and the UK with our dog every year for the past five years. This is what we have learned in that time:
1) Most hotels in France & Spain accept small dogs some will charge a small fee and some will charge nothing. IBIS (€5 per pet) & ETAP (no charge) all accept dogs. Just about every restaurant in France is okay with small dogs, Spain can be tricky unless it is summer when you can use the terrace.
2) We always get the ferry between Ibiza & Denia. We never ever ever put our dog in the cages aboard the boat as it would be too stressful for him. Instead we get a tranquiliser from the vet and leave him in the car to sleep his way across - an environment that he is comfortable with. We only ever get the fast ferry, it is more expensive but it means that he is only away from us for two and a half to three hours and it is less stressful for him.
3) Travelling to the UK we always use the tunnel. It's a little more expensive than the ferries but it is less stressful for the dog as you all stay in the car together and the journey is over and done with in forty minutes.
To the poster who asked if you can take dogs on planes; yes you can, however it is incredibly stressful for the dog and it costs twice as much as it does for a human.
The microchip problem sounds like an urban myth to me. When you get to the ferry terminal in Calais they give you the latest model reader and you find the chip; I doubt that there is any owner who cannot locate their dog's microchip (if in doubt, its location is printed on your dog's passport). If the microchip cannot be found then it probably means that the dog does not have one. At the point that the check occurs you have not checked through and are still in France. There is no "dog prison" in Calais, you haven't passed through any check-ins and can turn around and leave at any time. The only thing that you have to be aware of is that on your return to the UK you have to have had the dog's passport stamped by a vet to show that it has had a flea & tick treatment more than 24 hours but less than 48 hours before you check in. The DEFRA website gives you all the info that you need on this. Most vets in France and Spain will put whatever time or date that you want on the passport to fit in with your travel plans as they all consider the rules (which only apply to travel to Britain) to be a joke.
I'm sure that your dog will love her holiday in Ibiza just remember to pick up her poop (just because the Spanish leave it on the street is no excuse!) and not to let her onto beaches and she'll have a whale of a time, I know that ours does.
If you want to bring your dog to our bar, she'll be very welcome, just don't bring your kids who are not!