Hi Ben,
The short answer is "it depends on the nature of the small targets" and "I prefer a course with a balanced set of challenges."
On most modern course designs, small targets usually refers to greens with partitions of various sorts. Usually high and low areas on the green with ridges and mounds separating sections of the green. But it can also mean small greens, where the penalty for missing your spot is a hazard or an uncomfortable recovery shot.
Let's get theoretical about this for a minute. Let's compare this green with discrete, pinnable areas separated by ridges and mounds to a simple round, uniformly tilted green with no surrounding hazards. If we take a random distribution of shots to each type of green, I think you will find that the green with small discrete targets will exact a quantum penalty for missing the target, while the difficulty of holing out in two shots to a round, tilted green with no hazards is distributed in a more linear fashion. If you miss your target by 3-6 feet to the demanding undulating green, it might cost you a half a shot or more. If you miss by three feet on the simple green, it's just a .03 or .05 stroke penalty.
I think the modern undulating green with discrete pinnable areas has its place, especially in courses used for competitions, but there is value in a less contoured surface which levels the playing field between the expert and the average golfer. Furthermore, I find one of the most pleasurable plays in golf is a long, gently breaking and predictable approach putt. It's nice to have one or two of those every round.