The Futur I and Futur II tenses are not about the future but about assumptions. Consider:
Wo ist Jochen? — Er wird den Wagen waschen. (Präsens — Futur I)
Wo ist Jochen gewesen? — Er wird den Wagen gewaschen haben. (Perfekt — Futur II)
This isn't about the future. It's an assumption about what Jochen does right in this moment, respective what he did in the past. The speaker doesn't know it for sure but assumes it to be true. That's why she responds in Futur I / Futur II tense.
If she wanted to tell it as a fact, she would have responded in Präsens / Perfekt tense instead:
Wo ist Jochen? — Er wäscht den Wagen. (Präsens — Präsens)
Wo ist Jochen gewesen? — Er hat den Wagen gewaschen. (Perfekt — Perfekt)
And it's the same in your example:
Es wird seinen Grund haben.
This is Futur I tense because it's just an assumption. (Don't let the haben confuse you: it's a full verb in your example, not an auxiliary.)
Es hat seinen Grund.
This on the other hand is told as a fact.
Actually, all the German tenses are organized like that. Simple tenses for the non-past, perfect tenses for the past. There are seven pairs like that which differ in the intent of speech:
- Präsens / Perfekt — facts
- Präteritum / Plusquamperfekt — narration
- Futur I / Futur II — assumptions
- Konjunktiv I / Konjunktiv I Perfekt — hearsay
- Konjunktiv II / Konjunktiv II Perfekt — non-facts
- Konjunktiv I Futur I / Konjunktiv I Futur II — hearsay assumptions
- Konjunktiv II Futur I / Konjunktiv II Futur II — non-facts
That Konjunktiv I Futur I/II pair is seldom used. The Konjunktiv II Futur I/II pair on the other hand is the würden-replacement form of the Konjunktiv II / Konjunktiv II Perfekt. Konjunktiv II Futur I is used all the time as for most verbs you can't tell apart the Konjunktiv II form from the Präteritum form.
On top of that simple scheme, Northern speakers use Präteritum in place of Perfekt for the auxiliaries, the modals, and some very common verbs are e.g. geben. The more Northern the speaker is, the more verbs belong to this group.