My wife and I had a court marriage in 2003, with our parents’ blessing. However, only family members from my side signed as witnesses (3 people), as only 3 were needed. Could this cause any issues for my wife in the future?

As per the Special Marriage Act, 1954, your wife’s future legal rights are not affected by the lack of witnesses from her side. The presence of three witnesses in total, regardless of their relation to you, is sufficient for a valid court marriage.