Charging heats the battery, which adds to the heat that is caused while using the device. High temperature is bad for lithium batteries. Additionally, heavy load on the battery can mess with full charge detection, which can cause the battery to overcharge. Overcharging stresses the battery, which causes it to degrade faster. These won’t cause a lot of degradation, but if you want to prolong your batteries, you might want to keep these in mind.

But apparently, none of the above affects the Steam Deck. According to some internet posts, Steam Deck uses pass through charging. It means that while the device is connected to a charger, it will take power from the charger, and not from the battery.

What you should do, is to try to keep lithium batteries between 30% and 80% charge level. The closer to full you charge a lithium battery, the more it will degrade. And similarly, the deeper the discharges are, the more degradation is caused. Steam Deck has a charge limiter you can use to stop the charging at your preferred level.

https://batteryuniversity.com/article/bu-808-how-to-prolong-lithium-based-batteries

https://batteryuniversity.com/article/bu-415-how-to-charge-and-when-to-charge

EDIT: I have a power meter, and I just confirmed that Steam Deck, indeed, does take its power from a charger when one is connected. I charged the Deck up to the charge limit (75%) and then lowered the charge limit to 50%. After that, the charger was drawing about 0W while the Deck was off, about 10W while playing a 2D game (Hollow Knight: Silksong) and about 20W while playing a 3D game (FBC: Firebreak).

During charge, the charger drew 48W. The Steam Deck supposedly draws a maximum of 45W, which means my charger wastes 3 watts on a 45 watt load.