Yes.
Remember that decaffeinated coffee is coffee that has had caffeine content removed. To my knowledge, there is no such thing as naturally uncaffinated coffee. Since the coffee starts with caffeine and is sold to you without the caffeine, you can assume (rightly) that decaffeinated coffee undergoes more processing than "normal" coffee.
How do they do it, then? There are several ways in use today.
Chemical rinse. The (green) beans are steamed to heat and wet them, causing slight expansion. The beans are then rinsed with a chemical solvent that dissolves the caffeine. Unfortunately, this process also washes out a good bit of the oils and solid compounds that give coffee its flavor. That solution after flushing then needs to be treated to remove the chemical solvent. The beans are then reintroduced to the remaining solution, and the water is boiled away or allowed to evaporate, leaving behind the compounds that were flushed from the beans.
Water bath. The green beans are soaked in water and occasionally agitated for some time. The water dissolves most (but not all) of the caffeine. Then, the beans are removed from the water, and a similar chemical solvent to the chemical rinse method is used to dissolve the caffeine in the water. Finally, the beans are then treated just like the chemical rinse method. The resulting solution is treated to remove the chemical solvent, then the beans are reintroduced to the water for reduction and reapplication of coffee solids.
Filtering. This is similar to the water bath method, except instead of using a chemical solvent to remove the caffeine, a filter is used. The solution is passed through a filter repeatedly until measured caffeine content is minimal. This method of course removes some coffee solids also, since filters only discriminate based on molecule size. But caffeine molecules are relatively large, so this method is reasonably affective.
Carbon dioxide solvent. This method uses carbon dioxide to flush out caffeine by heating and applying high pressure to bring the CO2 to a supercritical state (where it acts as both a liquid and a gas). In this state, the CO2 is force at high pressure through the crevices of heated beans, where it dissolves caffeine (and mostly only caffeine) on contact. The CO2 solution is then purged from the beans and allowed to evaporate away, and the remaining coffee can be collected separately from the beans. Obviously this method is expensive and more technically challenging than the other two methods so isn't in common use.
Because there are different methods for removing caffeine from coffee and because each method requires a degree of precision to execute completely perfectly, approximation of the flavor of decaffeinated coffee to the flavor of the same, preprocessed coffee varies method to method and even batch to batch. In first two methods, for example, it's hard to ensure even distribution of the dissolved coffee compounds among the decaffeinated beans when reintroducing them. The other methods face similar challenges, except for CO2, which is, as I said above, just plain expensive. All of this means that even though decaffeinated coffee can taste mostly like regular coffee, it never will taste exactly like regular coffee. And whether it ever comes close enough is hard to say since the processes aren't perfectly consistent.
