For example, peace domain, which is a great subclass. But if we are 3 members overall, does it affect? 

Peace domain slaps no matter what the party size. Unless you have an excessive number.

It depends on the class and how they work.

Twilight Clerics have an ability that grants bonuses regardless of number - as a result, it gets better with larger parties.

Others use spells that usually targets individuals - for example, Cure Wounds, which makes the support character more potent rather than less with a smaller party.

The problem with support characters in small parties isn't so much their abilities scaling or not so much as they're reducing your other abilities. For example, a party of five will lose somewhat less than 20% in firepower, but a party of three will lose somewhat less than 33% of theirs.

That said, if you have a decent DM, they'll account for that so you can play the character you want to play (so long as you're not being daft and all three of you are trying to be healers).

D&D is such a malleable game that there is really no "wrong" or "worse" way to form a party. If you wanted to play a solo game as a cross-eyed toad with no class levels, then your DM could technically create a world and adventure appropriate for your abilities, or lack there of. The story adapts to the characters.

As already mentioned, group focused features benefit from having more targets, but there are multiple layers to being a "support" character. 1) Mechanical benefits and 2) Social benefits. With respect to the second, whether there are three members of the party or five, the people you play with are going to be equally appreciative of your contributions. Everyone likes getting to roll an extra die. It doesn't really matter how many people you're playing with. With respect to the first, there are plenty of ways to compensate for having fewer PCs, such as adding sidekicks, animal companions, or familiars. With the Peace Domain specifically, you can combine features like Emboldening Bond with spells like Summon Celestial to squeeze more out of the class.

Play what you enjoy, and work with the table and DM to smooth out the rest.

Play whatever you like. No matter the subclass you are still the base class. And there’s nothing wrong playing a support character no matter the size of the party.

And as others have said, the game isn’t strict to party makeup and the DM can adjust if needed. 

It depends more on the player than the (sub)class. If the player is content to sit back and focus on tossing out occasional heals, buffs, and debuffs, you'll notice the lack of major actions. If they're engaged and keep some regular damage options at the ready, they can fill in for whatever is needed at the time.

Take the cleric with Peace Domain. You are still a cleric with Command, Bless, Cure Wounds, Spiritual Weapon, Spirit Guardians, Hold Person, Silence, Dispel Magic, etc

No matter your subclass you still have access to a bunch of good spells that will help a party of any size. If you are a wizard, no matter your subclass, at low levels Sleep you can end an encounter with one cast. I don't see things like these as obstacles to helping a small or large party.