Does a pension refund affect future visas or citizenship?

No. The refund is a legal entitlement under German law, and claiming it is not held against you in any later visa application or naturalisation procedure. There is no register of people who took their contributions back, and no immigration authority asks about it. What the refund does end is your pension record: the refunded years stop counting toward any future German pension, and if you return to Germany later, you start building entitlements from zero. If a return with the goal of permanent residence or citizenship is realistic for you, weigh that record against the payout before you claim; the guide on returning to Germany after a refund walks through exactly that decision.