You only need one 10uF (or larger) cap on your board, preferably where power connects to the board. Every IC should have a 100n decoupling/bypass capacitor, usually on each of it's power pins, keeping any traces as short as possible. Some ICs, such as microprocessors, might benefit from also having a 10n cap in parallel with the 100n. In your case this is probably not essential for 16MHz but wouldn't hurt. It would be of more benefit for an IC such as a microprocessor that used a relatively low frequency external crystal (12 - 25 MHz) and multiplied that internally to a much higher frequency. Datasheets usually give some advice where decoupling caps are concerned, sometimes they even recommend a 10uF at the power pin of an IC in addition to the 100n and 10n.
Yes, THT is fine but again keep lead lengths as short as possible.
See! You can't mention 90 degree corners on a PCB forum without someone regurgitating this nonsense. But of course, if you prefer, there is nothing wrong with mitered corners.
We all know how power hungry those crystals can be! Crystal oscillator circuits are high impedance so wider traces aren't going to help there. The inductance of a 10 mil trace 0.5 inch long is 8nH, increasing the width of the trace to 20 mil gives an inductance of 7.69nH. Not exactly worth the effort. More importantly keep all other traces away from the oscillator area. As mentioned, some datasheets advise having a ground ring surrounding the oscillator circuit.
Having in circuit programming ability can be quite handy when you brick your board. Many processors also provide a JTAG interface for this purpose. You can always add the footprint for a connector to the PCB but not populate it until you need it. You'll learn how to use it quickly enough once you need to.
I can't make out much on the schematics you posted.