I am hesitate to use my 2nd attack because my clan war 10vs10 with score 28 stars(98.9%)-28 stars(96%) tight game (current winning in percentage, both have no more stronger attacks to score more stars). If I use my 2nd attack to loot already 3* base, will my attack affect total destruction % ? Please help. Thanks.
Clan wars are all about teamwork. If you use your 2nd attack to loot an already 3* base then it won't affect the total destruction % for your clan. The stars that you gain will of course be added to your profile but won't add up to the clan war score. You should still attack the base that is not 3* yet and just do your best in such situation rather than doing loot attacks.
You won't be affecting total destruction percentage if the base you choose to attack is already 3 stared (*). Just attack the base as Mehravish Temkar said which are not 3 starred. Here I would like to correct Mahravish Temkar: The stars you get on attacking a already 3* base does not add to your profile only new stars you obtain after attacking adds up. (I would have said this in comment but I don't have 50 reps).