Dear Bundy farmer,
the removal of stones, or to keep them depends on what you want to do with the farm. if you detonate or remove the stones and still there is some stone lying underneath the soil, please note that you cannot grow big plants.
If you feel that you can cultivate the whole land after the removal of all the stones and its worth the effort in terms of money, please go ahead.
If you are planning to remove the stones to make access ways etc, please get those removed. If the stony part is at an end of the farm and you need not visit it often, you can make a small hide out kind of a thing with some simple construction, and if you think its worthy, you can keep the stones.
If you need the stones for any kind of construction activity, then you can break them and use it for some constructions.
these change from case to case. Please introspect yourself what you want to do and go ahead.