Most - if not all - Arduino boards have serial connection to a PC, encapsulated in USB. The B in USB stands for Bus, so rather than a daisy-chain, it follows a bus topology. In other words, yes you can connect multiple Arduino's via USB, each of which is addressable from your PC as a serial device (maybe COM ports such as COM3, COM4 ring a bell).
But of course it would be easier to connect as many sensors as possible to a single Arduino. There are big Arduino's like Mega2560 that have a lot of digital and analog ports, but you could also look at analog or digital port multiplexers to share ports between sensors. Or look at sensors with a bus interface like I2C.
There are thermocouple amplifier ICs that output on the I2C bus (like MCP9600), so they effectively use only two arduino pins. Or you use 4051 type analog multiplexers, also for your analog flow rate sensors.
I don't understand how you get 3 pin fans with rotational sense, you will need 4 for that (VCC, GND, PWM, SENSE).
Anyway it looks like it is doable with only one Arduino, but your extra effort would go into handling the multiplexers. If you use multiple Arduino's on the USB bus your extra effort would go into handling muliple serial clients in the PC drivers and if you would daisy chain Arduinos via whatever serial scheme available, your effort would go into the dasiychaining code. So it depends a bit where you feel most comfortable.
That is, if it's just a prototype or a hobby project. If you want to design something that could potentially be sold or shared as open hard/software, I would try get it it all running on a single board.