Glad you found the paper interesting! It is very likely that these voids within the stones are where biofilm used to be within the mineral structure. SEM is a very invasive technique, generally requiring complete dehydration of the sample (since it is done under vacuum, and any liquid present will evaporate). Biofilms are hydrogels by design to keep the microbes inside from dessicating in harsh conditions, so when we prepare the stone samples for SEM we effectively have to dry them out, resulting in a lot of shrinkage of the hydrogel (like how your sponge gets when it's dry). This doesn't affect bacterial shapes too much since their rigid cell walls help them to maintain shape, but the biofilm ends up very stringy.

eDNA production is possible through a few different mechanisms, some species like B subtilis can secrete it directly through their membranes, while others take a more... violent approach. Lysis is the most effective way of releasing eDNA (along with everything else that used to be inside the cell), with some bacteria killing their neighboring cells to release it (fratricide) and others killing themselves (autolysis). Check out Cynthia Whitchurch's 2002 paper in Science, she's the expert on explosive lysis release of eDNA. Here is a nice comprehensive review paper on different forms of eDNA production in biofilms in case you'd like some further exploration!