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It is possible for familiars to have spell like abilities, either by virtue of being Improved Familiars, or from an archetype (such as Emissary), or both. Spell like abilities provoke attacks of opportunity but may be cast defensively as with spells; this requires a concentration check.
Even in weird cases, determining the DC of that check is fairly straightforward. Determining the bonus on the check, however, is not.
Let's take the example of a magus (with the familiar arcana) whose familiar has the emissary archetype, permitting it the use of guidance at will and a domain power SLA 1/day. The concentration check modifier has two components: caster level and casting ability modifier. Neither are explicitly defined.
Is the caster level for this purpose: 1) the actual HD of the familiar's base creature; 2) the master's HD, per the "effects related to number of Hit Dice" text of the Familiar Basics feature; 3) something else entirely, such as the minimum level needed to produce the equivalent spells?
Is the casting ability for this purpose: 1) the familiar's Charisma, as the default monster rules for SLAs; 2) the familiar's Wisdom, as these are derived from cleric features; 3) the familiar's Intelligence, because that is it's master's casting ability; 4) something else entirely?

Cevah |

The emissary gains Divine Guidance which states "An emissary can cast guidance at will." This means that the emissary is the caster, not the magus. The familiar bond affects the effective HD, and thus the CL. However, you use the familiar's stat for the mod.
The emissary gains Domain Influence which states "the emissary gains a spark of divine power from the patron that sent it". This is clearly a divine power, not arcane from the magus. For casting stat, clerics are not the only ones to get a domain. The caster with a domain uses their normal casting stat, which may not be Wisdom. Unless the familiar has some sort of caster level stated, you would use the monster default of Charisma. In any case, you would not default to the master's casting stat as they are not the caster.
/cevah

Melkiador |

As for spell like abilities that are native to the base creature, we don't exactly have an official ruling on that. At different times, different devs have ruled both ways. The basis for ruling against using the masters hit dice is that those abilities are based off of racial hit dice, but this makes an assumption that the effective hit dice for being a familiar are class based hit dice. The ruling for using the masters hit dice was already stated in the OP.