The Bible says the fervent prayer of the righteous is powerful and very effective (James 5:16). This means that when genuine born-again spouses, family members, friends, or associates pray, the Lord listens and hearkens to their voices. He loves to hear from them. One Word of prayer they utter on your behalf can change your life. However, if you are not yet born-again (i.e. surrendered your life to Jesus Christ), saying "Amen" to their prayers is like pouring water into a basket – it will amount to nothing. Why is this so? The Bible says the Lord does not listen to sinners (John 9:31). Whatever they utter in prayer is detestable to Him (Proverbs 28:9). Your own prayer, which is the uttered, "Amen" (meaning, "Let it be so") went unheard. Your loved ones heard it, but the Lord paid no attention to it.
Who are the "Sinners" referred to in John 9:31? Sinners are those who do not do the will of God. Those who continue to reject the salvation of Jesus Christ are also not doing the will of God. Master Jesus and the Bible in totality used the following terms for such individuals – "Sinners"; "The Wicked"; "The Rebellious Ones", and more. They are still under the dominion of Satan, whether they choose to believe it or not (1 John 3:10, 1 John 3:8, John 8:42).
Personally, when I know someone is not in Christ, and they say a word of prayer for me, such as: "God bless you"; "You are blessed"; "It is well with you," I smile out of courtesy without saying, "Amen". It is not that I do not appreciate their kindness - and I sincerely have no hard feelings, but who did they offer the prayer to really? In whose name have they offered it since they are not in Christ?
Albeit, our Lord is rich in mercy, not willing that anyone should perish. Surrender all to Jesus today to be an adopted child of God. You will then be a beneficiary of the prayers your loved ones is offering up for you, and in turn, be a blessing to others too with effective prayers.