Do instant-kill moves in Phantasy Star IV work better or worse depending on the enemy type?

Yes. All weapons and most techniques and skills are divided into one of 14 different attack categories. Each enemy has its sensitivity value, between 0 and 4, for each of these categories. Spark and EMP both lie in category 12, which is only effective (above 0) for mechanical enemies. Conversely, the Death ability won't work against mechanical enemies (sensitivity 0). Even within these creature types, the sensitivity varies from one creature to another, usually by 1 point (e.g. usually 2-3 for Spark et al.). Half the enemies in Nurvus are mechanical and have a sensitivity of 2 to Spark's category, which is why Spark is so effective there (that and Spark's high base effectiveness).

(Source. The explanation and table of attack types can be found under "Quantitative Analysis of Attacks". While the the list of monsters and their sensitivities is under "Monster Guide".)