Will pruning in KDX or the web wallet affect my Kaspa balance?

No — pruning only affects transaction history, not your balance. Your KAS balance is retrieved directly from the node on a per-address basis, and the node's balance data is never pruned. Pruning is a space-saving process where a node discards older block and transaction records while keeping enough data to know exactly how much Kaspa each address holds. So even if KDX or the web wallet does not show older transactions, your displayed balance will always be accurate.