As to why NPCs have these skills if they are not meant to influence and/or compel the decisions of PCs, first I would point to the odd man out, Deception. Unlike the other two social skills, Deception can apply in two slightly different situations. The first, the typical social interaction check, is one in which a character is attempting to influence another creature in order to gain the creature's compliance with some request or demand. If that attempt is based on a falsehood, then skill in Deception would apply. A PC cannot be influenced by such a check because the premise of roleplaying is that the player assumes the role of his or her character. A PC's actions cannot determined by such a check because they depend solely on the decisions of the player. Persuasion and Intimidation are likewise unable to influence the player's decisions with respect to his or her PC. The best way to resolve such a situation is for the DM, as the NPC, to lie to the player, and for the player to decide on the PC's response. No check, and therefore no skill, need be involved.
On the other hand, if the player suspects a falsehood, and seeks to verify the truthfulness of the NPC's statement through observations of the NPC's body language, etc, and the DM asks for a Wisdom (Insight) check from the PC, then this can be contested by the NPC's Charisma (Deception) check. The outcome of this check, however, does not determine whether the PC is compelled to any sort of action if the lie is found to be believable, but only whether falseness is in fact detected.
Looking at the DM's Basic Rules, the four monsters/NPCs skilled in Deception are the Doppelganger, Medusa, Green Dragon, and Cultist. All of them are figures who are likely to lie to the PCs. Their skill in Deception will not come up however unless they attempt to deceive other NPCs, or if a PC attempts to uncover their falsehood.
Intimidation and Persuasion are both very similar to one another in that they both represent an attempt to influence through force of personality without resorting to falsehood. Intimidation is backed up with threats, and Persuasion is supported by good manners, or compelling arguments. There is no action that parallels the discovery of falsehood in the case of an interaction that relies on these skills, so if an NPC is attempting to persuade or intimidate a PC, no check is required. The outcome depends solely on the player's decision.
Orcs and Thugs make a Charisma (Intimidation) check to keep their own allies, or lesser creatures, in line, given that social skills are more effective when used on friendly creatures. Likewise, a Priest will use his skill in Persuasion, not to boost a Charisma check the outcome of which will determine the PCs actions, but rather to influence the actions of of another NPC. If the PCs take action to elicit the opposite outcome, as [MENTION=97077]iserith[/MENTION] has pointed out, these become contested checks.