Honey contains lots of aromatic compounds, which are quite big, fragile molecules. This is one of the reasons why cold centrifuged honey costs more. When you decrystalize honey by heating it, many of these aromatic molecules break up, and you lose the complexity of the aromas. So yes, it is bad for the honey. Also, it may reduce its health benefits, as vitamins and other micronutrients tend to degrade under heat (but only some of them - others, like trace minerals, are quite unimpressed by temperature).
Of course, the question is not only if it is bad, but if it is worse than eating crystalized honey. This depends on 1. The honey quality and 2. the way you plan to use the honey. With the honey quality, it is obvious that, if the honey has already been heated in the production process, the volatile stuff has already been destroyed, so subsequent heating for decrystalization is not a problem. But if you spent money on cold centrifuged honey, you are negating its benefits by heating it.
About the use: If you will heat it anyway (as in putting it in tea, or baking it into a dough), there is no reason not to decrystalize first. Also, if you are only using it as a sweetener, even cold, there is no problem in heating it. But if you are using it as an aromatic agent, like in a creme fraîche and honey dressing for a fruit salad, or using it as a bread spread, then it will taste better if never heated. It will still have a general honey taste and aroma, but the subtle notes will be missing. Whether this bothers you or not depends on whether you rate aroma or texture higher. My personal choice is to not heat honey in these cases, but your preference might be different. Probably the best way to decide is to take a small amount of crystalized good quality honey, heat it, and compare it side-by-side with the crystalized version. Then use whatever version you like better.
If you happen to like the decrystalized one more, it is probably a good idea to not spend money on fancy honeys in the future ("cold-centrifuged lavender honey from South France" etc.), as it won't taste all that different from a common wildflower honey after decrystalization.