Tools like Smith's Hammer and Pick Axe etc. have a "uses remaining" limit to them. When the "uses remaining" get down to 1 or so, can repairs be made to it to bring it back to or near its previous total-use count? Or basically will i just have to buy a new tool?

Your best bet is to get basic tinkering that way you can make the tools your self, as far as i am aware once the charges are down they are down.. You don't need very high tinkering to make pick axes and hammers etc and is well worth having with a blacksmith/crafter

once the "uses" are used, the item is destroyed/disappeared. I agree with Archaon though, definitely work tinkering a little to be able to make your own tools.

In todays markets its sometimes cheaper to buy the tools than to create your own, because ingots are worth more.

Is there a benefit from buying crafted tools over npc tools?

The only benefit would be the increased number of uses. An exceptional tool can yeild over 100 uses, as opposed to a npc hammer of 32 uses.

and plus if you mine your ingots you do not need pay for ingots or tool, as you will mine the ore, smelt them to the ingots and use them to make tools and weapons/armour and as leepin' Leezard said when you make exceptional it can have over 100 uses which is cool

Repairs can only be done on a weapon or tool damaged in combat, not worn out from being used as a tool. Two different sets of numbers are involved: the number of uses, which indicates tool usage, and which goes down after every successful use; and durability, expressed as a pair of numbers 36/36 for example, which will go down when damaged in combat.

As has been said, it's cheaper and quicker to make your own tools using the Tinkering skill. Normal quality tinkered tools have 50 uses, exceptional tinkered tools have 100 uses (numbers on Siege Perilous are a bit higher). Also, if you become involved in the Blacksmith BOD (Bulk Order Deed) system, you will soon have a large supply of tools, at least for mining. These shovels and picks have even more uses than GM tinkered tools, 150 or 200 uses being typical.