You don't HAVE to fill the bottom slots, the thing is, if you don't your reforge might fail.
Failing is bad, because usually if you are reforging, the stat providing tool is probably one that have a stat that you want and the stat is fairly high, losing that might really hurt.
On a side note, exp pigs, especially the silver one, provide more % chance than a regular tool, so it is possible to get to 100% chance without having all slots filled.

As for the reforge itself, what it does is this:
You have a target tool and a stat provider tool
You select one of the stat of the stat provider tool
If the target tool does NOT have this stat already, you can replace any of its stat*
If the target tool already have this stat type, you must replace the existing one
Then you click reforge, and if successful, the stat you want will replace the stat of the slot you choose.

You only get ONE stat per reforge, so an awesome tool with say +80 attack AND +80 nin probably should be the basis of the reforge, as you cannot use it to reforge another tool and have both of those stat go over.
You may reforge any tool with any other tool, slot does not matter, color does not matter.
elemental resistance are considered as different stats from each other, so you could, if you really want, have +4 resistance to every element on every tool (+40 resistance to all element), thou that will take up almost all (5/6) of the stat slots.


*any of the stat including an empty one, gold tool can have up to 6, not sure about the other colors, so if it's a gold tool of 5 stats, you can select an empty one to "add" the stat to it

No
You can reforge at anytime, thou since items might be replaced later, it's probably not worth the effort until you are on the final tier of golds tools

Also, as it's easier to get a good set of elemental connection if you have multiple tool of each type(slot) with different elements, you might want to delay reforge until you have elemental sorted(as having a fixed set of tool that you have to elemental for instead of 3-4 sets of replaceable puzzle parts will increase the cost of getting perfect elemental connection by 5-20 times, depending on what you are aiming for, in terms of elemental stones)

currently, due to lack of red elemental stone, the ideal tool is the highest tier gold tool (the one with the most base stat), reforged with red gourds and have gold matching elements with its neighbors.

As it stand, even if new red tools are released, the only thing they would have over this configuration would be a higher base stat, which comparing our best gold gourd vs the "red gourd" is fairly minor. And unless it comes with red elemental stone in the same TI, gold tools with reforged "red" secondary stat w/ elements will still be better than red ones w/o elements

So no, the concern for future release is less than what you thing it is.