Brand new laptop, two years in storage, will the battery be ok?

Lithium-ion cells age the moment they leave the factory, plus the ~500 cycles they can do (to 80% capacity considered EOL). That means the batteries in the long termed stored laptop will be degraded, even without having been cycled or used.

If it was properly stored, which preferably would be not in the device, stored at 40-60% charge level prior to being stored. Stored in lower temperatures, like room temperature and below, being left in a garage getting 100°F temperatures would have it degrade faster.

Some Li-ion pack protection, and balance (if existing) circuits will drain a pack (very very slowly), that happens more often in series packs (yes laptop kind). If when you get it out it has NOT drained down to very low, then you do not have that problem. If it has drained out below proper spec lows for the cells in it, it could be in very bad shape, even a pack that would be considered dangerous. (Formation of bad things internal to the cell that causes more heating on charge.)

That leaves the question of how bad will it be? Depends completely on the cells used in the pack originally, how long the cells were already sitting around before it was built/sold. Plus temperatures and charge state (as mentioned) when stored.
Li-ion cells have a life ranging from ~2 years for poor quality ones, to unheard of ~10 year lifespans for some rare cells of good brands that are cared for in every possible way. An average life is somewhere around ~3 years to 80% capacity, after that it is considered to be finished. (They become slightly less safe and harder to balance and prone to other issues after that.)

When you get it out, see if it is holding some charge, making a first whole 100% charge on it could be important (if it has balancing). Check to see that the battery is not heating up badly when charging. When you go to use it, if it does not run for the appropriate time, it is possible a few charges will help. Cycling Li-ion is not supposed to do anything to help them, but some low-quality cells do better after a few cycles.
If the battery pack is ever getting really hot, or performs poorly, it would be better to replace it than to see what happens next :-) Unsealed cells release toxic stench, cells that way overheat can cause laptop fires and shoot across the room with flames and all. Really bad stuff while rarely happening with Li-ion happens more often with bad cells, and can start other things on fire, messing up your whole day :-)

The lithium coin cell is a primary lithium cell, not a Li-ion. They are normally good for 10 years, and could keep the CMOS settings and clock viable for at least 5 years. It should not be a problem, but the first time you have access to it (like when cleaning), it wouldn't hurt to change it. If you're losing CMOS settings, then you would have to.

If the battery was really brand new from the factory, it will have self-discharged (typically at the rate of 1%/month) and need recharging, but since it has only undergone one discharge cycle, it will be OK, as Li-Ion batteries still deliver 80% of their original rated capacity after 300 charge-discharge cycles, and are rated at 400-1,200 cycles before replacement is necessary.

The CMOS battery on the motherboard may have also run down, and you may need to go into the BIOS to reset its date.