Using your tree for bonsai will not have any effect on it's reproduction. You can still propagate the unwanted branches and shoots into cuttings for rooting or plant the seeds from it's fruit / flowers Etc. All that matters is that your particular tree species is capable of reproducing.

So, that means if I bonsai my silver maple, it will still send out those little helicopter seeds and still be viable?

IF you are going to bonsai a silver maple just understand that it is not a very favorable maple to use. The leaves do not reduce well and the branches tend to have long internodes. Your tree would need to have a relatively large final size to work out. They also tend to drop branches like crazy which is another poor trait for bonsai as the tree can just randomly ruin the branch structure you have worked so hard for. Otherwise, if you let it grow long enough and it is healthy it should still fruit (make helicopters). Even if you can reduce the leaves and branch structure, fruit never reduces so the helicopters will still be the same huge size as opposed to JM or Amur maple. I believe a maple also requires enough trimming that you do not normally get flower/fruit. I've never seen them on any bonsai maple I've seen presented. Finally, seedlings can take a very long time to fruit. Silver maple is one of the faster growing trees but I have no idea how old they usually are before fruit (wisteria seedlings can take 15-20 years).

But yes it still will. People grow things like flowering cherry, crabapple and dwarf pomegranite all the time for bonsai.

Okay, I have a White Pine, some Silver Maples, Sumac Tree, Black Locust and an Apple tree. Would any of these work easily as a bonsai? Thanks in advanced.

While most of those are "native" or at least more acclimated, none of them are particularly suited for bonsai. Mostly due to large leaves or long internodes. The (Eastern) White Pine has long needles but have been used. There are a few out there you can find by searching. The Silver Maple has large leaves that don't like to reduce and they drop branches like crazy. Sumac, not sure. Black Locust has compound leaves but might work on a larger tree. Apple could be used but if you ever let it fruit it's still going to grow a full sized apple stressing on a tiny tree. This doesn't mean throw them out. I have played with what ever is around for years. This year however I have narrowed my focus to quality over quantity. I did destroy my Silver Maples and Eastern Red Cedars. I just don't have time for stock that's never going to look good. But I did learn about chopping and pinching from these beginning trees.

I forgot to mention I also have a Lemon tree I grew from seed. Would that work?

A quick search shows that they are done, maybe more as a commercial gimmick than a serious tree. I'm assuming that means the leaves will reduce but once again, the fruit is not going to. So if it was a dwarf lemon that quality might have come through but otherwise you will be stuck with large fruit. Grow it for the foliage or the trunk.