Why this happen?
Valorant is just one game developed by Riot Games, whereas the Riot Client is a client through which you can launch any game provided by them, currently including: League of Legends, Legends of Runeterra, Team Fight Tactics, and Valorant.
When you install any Riot game, the Riot Client is automatically installed, it is designed to open, close, and update the games. It also simplifies the login process since all games are accessed through the same Riot account.
Answering your questions:
Is this common/has this happened to anyone else?
This is a bug that occurs in Epic Games due to the installation itself already creating shortcuts, but Epic recreates them, resulting in 4 shortcuts instead of 2. The correct setup should have one shortcut for the Riot Client (with the Riot symbol) and another for the game you installed (with the symbol of the respective game).
Which shortcuts should I use?
It depends on what you want to do. If you want to launch more than one Riot game or play a game while another is updating, you can open the Riot Client, if you only want to play Valorant, use its shortcut.
It's important to note that even if you use a game shortcut directly, the Riot Client will always open (if it's not already open).
Would anything bad happen if I deleted one of each duplicate shortcut?
No, deleting it doesn't affect anything.