This always takes time. It sounds like they are doing very well with their new home and this is all very new to them. It also depends on the piggy however there's always going to be some times when they are jumpy and some more then others.
Their hideys are their safe places and will help them adjust and trust their environment. The only time I've removed a hidey is the igloo when the weather can get too hot. Otherwise let them have their security. There are many pig whispering tips and links even here on this forum. It sounds as if you are doing just fine, really. They will eventually trust you each at their own level and it does take some time. Just give them treats, approach them with some noise and gentle talking as not to startle them and enjoy getting to watch your piggies develop some unique character together.
Welcome to the forum and the wonderful world of guinea pigs!