Is it ok to lay engines on their sides in storage for long periods (years) of time? I am worried about oil leakage etc.
There should not be enough oil in an engine to leak. The gearboxes are usually packed very lightly with white lithium grease, which hardens over time but will not run out under normal temperature conditions. Some locomotives sit on dealer shelves for years and years without leaking in their boxes, so if you have not over-oiled your locomotives there should be no problem.
After this long-term storage, I would clean and re-lubricate them before operation.