It's not necessarily bad to pluck to 5 pikmin. You can just pluck cancel the last one.
You'll learn to listen for the plucks and the timing of the presses with time. Don't worry.
Also, one thing you can do if you have five pikmin and want to check if you have one off the top of the screen (like if it was blasted up by a move) while on the run or if you aren't certain if you plucked to five or six after respawning is you can try to ledge pluck the last one. There's no lag for a whiffed animation when you do so and it's a nice, quick check. Very niche use, but still useful.
For example: You respawn on BF, accidentally pluck two instead of three, and ledge pluck the last one while testing as you get down from the top platform.
On another note, it kind of feels like I'm atrophying as a player. Can't go to tournaments until January or February, Austin's best player doesn't go to fests (and when he does, he doesn't use Yoshi), and most of the other players don't pose much of an actual challenge. It's so frustrating. :<