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Usually if something goes wrong during seed production, some extra tissue is found inside the vegetable (which is edible). These seeds pictured look like they are swollen with water. I did some research and found that if cucumbers don't get enough water, they put all their resources into their seeds (and they are primarily water).

The article below says the chance of grocery store seeds germinating and growing is slim. Even the organic vegetables are likely hybrids. If they are "heirlooms" you should be OK. Same problems on the peppers.

https://www.gardeningknowhow.com/edible/vegetables/cucumber/plants-from-produce-cucumber.htm

https://www.gardeningknowhow.com/edible/vegetables/cucumber/cucumber-seed-harvesting.htm

https://www.gardeningknowhow.com/edible/vegetables/pepper/store-bought-pepper-seeds.htm

If they are growing just fine and have enough light, I would keep doing what you are doing and let them grow. If they start getting leggy you can pinch them back. (or in the case of zucchini the article below says to add soil)

https://www.gardeningknowhow.com/edible/vegetables/cucumber/pruning-cucumber-plants.htm

https://www.gardeningknowhow.com/edible/vegetables/zucchini/zucchini-plant-falls-over.htm

Absolutely! I do, every year! You will need to hand pollinate if these are indoors, and watch your soil moisture levels, carefully. It changes much faster than it would if they were in the ground. Trellis them, as well. It helps save space!

https://www.gardeningknowhow.com/edible/vegetables/cucumber/cucumbers-in-containers.htm

https://www.gardeningknowhow.com/edible/vegetables/cucumber

https://www.gardeningknowhow.com/edible/vegetables/squash/growing-squash-in-containers.htm

https://www.gardeningknowhow.com/edible/vegetables/squash

Damping off is usually caused by fungal or bacterial infections. Typically, this originates from wet soil conditions, so if it was accidentally overwatered at one time, then this could be the source. Soils that are too compact will have this issue, as well.

https://www.gardeningknowhow.com/garden-how-to/propagation/seeds/what-is-damping-off.htm

Are they getting six to eight hours of sun each day, regular fertilizer and water? Here are some articles that should help:

https://www.gardeningknowhow.com/edible/vegetables/tomato/yellow-tomato-leaves.htm

https://www.gardeningknowhow.com/edible/vegetables/squash/why-squash-leaves-turn-yellow.htm

https://www.gardeningknowhow.com/edible/vegetables/cucumber/tips-for-growing-cucumbers.htm

Technically, you can space them a, mere, 2 or 3 inches apart! As long as they have the run of about 3 feet, then you can crowd them and force them down the hill.

Unless they are crowding each other, then it will not be necessary.

Here is an article to help you with cucumber care:

https://www.gardeningknowhow.com/edible/vegetables/cucumber/tips-for-growing-cucumbers.htm

Here is a nifty spacing chart that will be useful in the future:

https://www.gardeningknowhow.com/edible/vegetables/vgen/plant-spacing-chart.htm