If a plum flower is pollinated by peach pollen, the flower will still produce a plum (fruit), it is until you plant the seed....then the seed will germinate and finally a hybrid tree is produced.

So the answer is yes, you could plant a sweet and a sour cherry together without having to worry that they will produce hybrid fruits by just getting pollinated (flowers) by another pollen source.

If you have limited space, you could plant multi-graft trees.

I don't believe you are correct about cucumbers and watermelon, unless you are collecting seed. Cross pollination changes the seed, not the fruit, so it can be a problem with hot and sweet peppers and corn but not the fruit or leaf part of plants.

It's a common old wives' tale that different species of vine crops cross. Cucumbers and watermelons don't have compatible pollen, so even if you were saving your own seed year after year you still wouldn't have problems growing cucumbers and watermelons side by side. Watermelons don't even cross with muskmelons/cantaloupes. I have personally been growing watermelons and cucumbers and saving my own seed for years, so I'm speaking from experience, not just book knowledge (and I've read the seed saving books, too.) There are some plants that will cross between closely related species. Tabasco peppers and habanero peppers and jalapeno+bell peppers are 3 different species, but limited crossing can allegedly take place between those species. There are other plants that we think of as different but that are just different selections from within the same species that very readily cross, like cabbage with brussel sprouts with broccoli with collards... but crossing between actually different garden crop species is very rare.

To the original question, I can think of very few instances where there would be any pollination-related disadvantages to planting one kind of tree near another. Growing some kinds of persimmons might cause other persimmons to grow seeded instead of seedless fruit. If you wanted to try to breed new varieties of fruit trees in any kind of controlled way you'd have to control pollination, but I assume pretty much everyone that's actually breeding new varieties of fruit trees in controlled ways does so by bagging flowers and hand-pollinating such that it still wouldn't matter what's planted where.

If you're a beginner, I think the short answer is that there really isn't anything you shouldn't plant because of pollination, but there are things you will need to plant for cross-pollination. A lot of fruit trees are self-incompatible, meaning the pollen from a tree won't pollinate the flowers from that same tree, so you'd need at least two separate varieties, generally from within the same species to pollinate each other. Sweet cherries and sour cherries are separate species, and so far as I know, won't cross at all, but maybe someone that knows more about cherries can say more about that. As harvestman said, when trees cross-pollinate that doesn't change the fruit; it only affects what kind of fruit you'd get if you took the seed from that fruit and grew another tree and it fruited, and generally speaking that's not how any of the common tree fruits are propagated anyway, so it's a non-issue for all typical backyard or commercial growers.