The ESP32-S3-MINI-1 has 39 GPIO pins, though the data sheet defines that one (GPIO26) is reserved when using PSRAM (e.g. ESP32-S3-MINI-1-N4R2).
Unlike the S1 boards, the GPIO are all available as input or output, making its very flexible. But as always there are some caveats on GPIO usage.
The following relates specifically to the ESP32-S3-MINI-1 module only.
GPIO0 is the main strapping pin that defines BOOT mode. If low at startup the device enters boot mode. It is pulled up internally so can be left unconnected. This means you cannot use this as an input if there is any chance of the input being low at start up. It can be freely used as an output.
By far the most common usage for GPIO0 is connection to the cathode of a status LED.
By default these are USB. This may make them not ideal to use for inputs. Note that they can be configured not to be USB by a fuse setting, but will be USB on an unconfigured module. As such it is probably best to use for USB.
The cannot be used with a PSRAM module, e.g. ESP32-S3-MINI-1-N4R2. It can be used if not PSRAM, e.g. ESP32-S3-MINI-1-N8.
By default the boot serial console uses GPIO43 and GPIO44. This means GPIO43 is configured as an output at start up. There are settings to stop any actual output on this. This means it cannot be used as a driven input without at least a resistor to handle the clash at startup. GPIO44 is an input so can be used for any purpose without any problems generally.
GPIO46 only matters when in BOOT mode (GPIO0 low) and in such case must be low. It is pulled low by default so an be unconnected. But do not use this as an input that could be high at startup in BOOT mode. It can safely be used as an output.
This is defined as a strapping pin, and is floating by default. However it is only relevant depending with some specific eFuse settings related to JTAG operation. When using the default USB JTAG working, this pin can be used as a general input or output.
GPIO46 impacts the voltage used for SPI, but depends on EFUSE_VDD_SPI_FORCE. But this efuse is already set by default on this module, which means GPIO45 is ignored. It can therefore be used as an input or output.
Serial or USB console?
The S3 modules have two ways you can operate the console - the normal serial (UART), and USB.
The default USB working is as USB JTAG and Serial console. This allows flashing and debug console, and a lot more debugging using JTAG and OpenOCD. This is by far the simplest way to manage the module and what I would recommend.
In most cases my boards have USB, either a printed tab for USB-A or a USB-C connector, but in the rare cases they do not, it is simple to include a header for USB to work with a lead.
This nicely fits under the module itself, with no vias, so takes no space and so no component cost. I deliberately spaced as 0.1" header and with a polarity to avoid confusion.
Apart from using JTAG, the USB serial is not really serial, so is way quicker for flashing code than using the real serial port.
There is one small snag...
It is possible to use an efuse, and more importantly, it is possible for the application to turn off the USB pins. This can even be inadvertent (I have done this, loading code for a different board which had an LED on GPIO19). This then means you cannot use the USB port at all, so cannot reset or load code or anything.
For this one reason, it is always useful to have a fallback.
The other approach for flashing and console is the conventional serial port. For this you need to have at least Tx and Rx (GPIO43/44) pins, and boot mode (GPIO0), and a means to reset (EN). You could use power on as the reset and keep it to just 5 pins. I use a header that works the same as the Shelly 1 and so can use my Tasmotiser board.
This also fits under the processor rather nicely with no need for vias, and no component cost. In fact, it can fit under the processor along with a USB header...