Ancestry has never guaranteed the storage of their Y-DNA/mt-DNA samples. Those of us who transferred from Relative Genetics knew this. However, the accuracy of testing at Sorenson Genomics was a primary consideration at the time.
The low-res mt-DNA test is largely a waste of money. You can get hi-res female haplogroups from autosomal testing at 23andMe. If a researcher wants to use it in a genealogical time frame, he would need to take the full-sequence test at FTDNA. However, it is of very limited value, due to the generational surname change on the distaff side.
The next step in Y-DNA testing is the full-sequence test. I doubt that there is a enough DNA left at Ancestry/Sorenson for these tests. It is likely that researchers will need to recruit other participants to replace the DNA of deceased project members. There is also possibly a legal problem with using a deceased's DNA. FTDNA has done much to address the problem.
I applaud Ancestry's decision to concentrate on paper documentation and autosomal testing. I have been involved with DNA testing since 2000. It is very effective at determining which people may be related. or, more importantly, not possibly related. However, in the end, we need paper documentation to determine the exact relationship.