Floating row covers will aid in keeping insect pests from those plants, but will also keep the pollinators away. Where you use them may require hand pollination to get the fruits plants want to produce.

I know for the squash, you have to uncover it to get it pollenated, I'm not sure on the eggplant though.

Remember that if you are opening up the cover to hand pollinate, you might just be letting pests in then and then trapping them there if you re-cover things.

It is possible to hand pollinate squash and probably eggplant as well but at that point, you might be better off uncovering the row and depending on the type of pest, applying the appropriate organic control. Like Thuricide or Dipel against caterpillars. Soap sprays against aphids or whitefly nymphs. Neem or garlic sprays against some other problems (though neem and garlic can be toxic to bees so you should be careful there.)

I think the row covers are mainly for young plants, non fruiting crops, or sometimes season extension.

Here is a link that might be useful: TCLynx Gardening

I have been using row covers extensively for over 15 years. I use them year round on all sorts of crops.

yes you have to open them up for pollination. you can deal with this two ways.
1) remove the covers when the plant has gone into flower and leave the covers off
2) keep the covers on and hand pollinate

I have found that row covers with drip irrigation/soaker hoses keeps most the moisture where you want it-in the soil by your crops. Without the row covers you will lose most of your moisture, even with mulch on the ground.

I also have found that row covers give one the out of sight, out of mind mindset often and if you use them you must check underneath at least every other day. if you don't and pests get in there you will have a big problem on your hands as the row covers make for about perfect conditions for pests.