Yes, one of the reasons for using 2-layer PCBs is to avoid the jump wires. On a complex board there would be lots of them in all directions. Your layout doesn't need the second layer, though; it's still simple enough to be routed on a single layer without wire bridges. If you get stuck you may have to move some components to another position, but it can be done.
I would suggest to try it instead of going the easy way of the 2-layer board. It's about practice. If you don't succeed in doing this on a single layer, you'll never be able to do a more complex board on a 2-layer PCB either.
A professionally made multilayer PCB will have copper-plated vias to connect the top trace with the bottom trace. If you plan to make the PCB yourself you won't have the through-metallization, but since you only use PTH parts you can solve that by soldering the wires on both sides of the board. For some components the wire may not be reachable on the component side. Just make sure there's no trace to the hole on that side then. If you would need vias apart from the components' mounting holes you can solder a thin wire on both sides of the hole.
2-layer PCBs will often use both layers for routing, and even component placement. On densely populated boards this may not leave much room for copper planes, like for ground or Vcc. If these are really required designers often will go to a 4-layer board. A ground plane not only helps in the design of HF designs, but ground is often the net with the most connections, so it takes a lot of routing away from the outer layers as well.
Today most PCBs use SMT technology, and SMDs will often be placed on both sides of the board. First the components on one side are fixed with glue dots, then the board is flipped and the parts on the other side are placed. The glue is needed to avoid the components falling of when the board is turned upside down. Some glue dot machines can place up to 50000 glue dots per hour, that's 14 per second!
Vendors are not good at telling you how costs will vary based on different specifications. They will always ask you for your files and provide a quote to that specific board. They generally can't, or won't, give you a relative answer. In my experience the number of vias is not as important as the size or type. Microvias (definitions may vary from vendor to vendor) are much smaller and will cost more than a standard via. Blind vias (which do not extend through the entire board) will also be more expensive. The price difference between having 200 vias and 100 is probably going to be negligible. Back when holes were drilled manually the cost would have been impacted much more, but nowadays with machines doing all the work, it really doesn't make much of a difference. Keep your via diameters large whenever possible, though. If there's a higher chance of a bit breaking (because it's so small), the board house will charge you more for the fab.
Best Answer
Full tenting is normal. You will be fine if you fully tent all vias. It will not have any impact on cost.
Why would anyone ever leave vias untented?
Well, sometimes people leave some vias untented on prototype boards to facilitate probing signals. But vias near pins or pads should always be tented. Vias which are underneath components cannot be probed or visually inspected, and so they should always be tented, too. If you want to leave other vias untented, that is up to you.