It seems that logistically speaking, the Deathwatch have a major hurdle to overcome, due to the fact that bolters used by Space Marines use different types of bolt shells that are incompatible with Imperial Guard bolters. So resupply seems like it should be a major issue for Deathwatch Marines, since unless their is already a Space Marine presence in their theatre of operations, it should be almost impossible to resupply on bolter ammunition in the field.
For example, I'm having a hard time seeing how supply dumps in Final Sanction would allow them to resupply on bolter ammo, considering the above about incompatibility issues with Imperial Guard bolters.