If there are several enemies knocked airborne together (for example with Malphite's ultimate), Last Breath will automatically hit all of them. Is it possible to click a single target and only affect that one?
No, you cannot affect only a single target.
From the League of Legends Wiki:
Range: 1200 - Cooldown: 80 / 55 / 30 - Physical damage: 200 / 300 / 400 (+ 150% bonus AD)
ACTIVE: Yasuo blinks to the nearest visible Airborne enemy champion to the cursor, instantly generating maximum Flow. Upon arriving, he suspends all airborne units within a 400-radius of his target in the air for 1 second.
Once he lands, Yasuo deals physical damage to all nearby units and gains 50% bonus armor penetration for 15 seconds (this affects armor from items, buffs, runes and masteries, but not armor innate to units). Casting Last Breath will reset Steel Tempest's chain.
As mentioned in the skill description, Yasuo will strike all airborne champions within 400 units of the closest airborne unit at the time the ability is activated.
In general, no, there is no way to cast Last Breath on a specific target and avoid other targets within range. However, you can influence the targeting, which in some cases could change the number of enemies affected.
Last Breath is auto-targeted, and can only be cast when an airborne enemy champion is in range (1200 units). The primary target is automatically selected as the nearest airborne enemy champion to your cursor, and Last Breath affects all airborne enemies within a 400 unit radius of the primary target.
As such, if multiple enemy units are airborne and more than 400 units away from each other, you can choose where to cast the spell. If three airborne enemies were in a line, each 300 units from each other, you could hit them all by casting on the middle champion, or you could miss one from the end by casting on the champion at the opposite end.