If the small hall bath is on the main level of the house, I would not turn it into a linen closet. Most buyers prefer to have at least a powder room/half bath on the main floor for convenience. However, if there is a shower there than it would not hinder the value of the property unless there is a first floor master bedroom. Most buyers that are looking for a first floor master desire a full bath as well because of convenience.
Therefore if all three bathrooms are on the 2nd floor then it would not devaluate the value of the property by much by converting to a half bath and removing the shower. Normally, there is a definite value by increasing the number of baths but the location can also be important.
However, keep in mind you are the one living in the house, so you can do what you want! That is the privilege of home ownership!You can always convert the linen closet back to a bath when you go to sell!
The more baths tend to itself to higher value but since you will be the owner you can do anything you want with the home to accommodate your family's needs. when it comes time to sell it you can convert it back if you would like.
Good luck on your purchase.