Changu lake permit is obtained in tsomgo lake police check post. You could apply online or through a tour operator. Nathula pass permit can be obtained in Nathula check post. From what I gathered through known travellers is this lake is not closed on public holidays.
Tsomgo (Changu) Lake and Baba Mandir permits are issued at the Police Check Post. Foreigners can also get it at Sikkim Tourism & Civil Aviation Department. Easiest is to apply through a travel agent or tour operator one day in advance