Maybe. There are four 4-pin fan headers capable of either PWM or voltage control (3-pin fans). With the correct splitters you're fine there. Most splitters have the tacho wire connected to all fans so the reading is garbage. You need to pick one fan in the group and have the tacho wire connected only to that one.
Water temp sensors: no problem. There are 8 temp sensor headers. You can connect inline water temp sensors or tape the sensors (4 supplied with Aquaero) to things you want to monitor. I have one taped to my pump heatsink to keep an eye on it and one on each of my toasty M.2 SSDs. The stuff you want to tape it down is Kapton tape (or a cheap foreign knock-off).
Flow sensors: depends how they connect. There is a header labelled "Flow" on the Aquaero. This takes a connection to the Hi Flow sensor. The square block style one without USB that's about £30 on OCUK. Be aware that it requires a separate cable (helpfully not supplied) to plug it in. It looks like a fan plug but the pins are much bigger.
For a second flow sensor (which will read the same unless you have dual loop or a parallel flow section ) you can either use one that connects by Aquabus or USB. You could add a PowerAdjust Standard which has a flow header on it and a 3-pin volt controlled fan header.
Pumps: you can definitely run them off the Aquaero but there are considerations here. If they are 3-pin you can run one off each of two fan headers. You might be able to run both off one but you need to be careful you aren't overloading the header which has a 30W max. You'd probably need either a cable convertor (there's a DDC cable available) to change the mole and fan connector into just a fan connector. That or crimp some fan pins on the end instead (and braid it
).
If they are PWM it has been reported that the D5s don't implement it correctly and need a mod before they work. The Aqua Computer ones are apparently pre-modded.
If you want to run both of one header it should be fine as it doesn't pull the power from the Aquaero (unless you mod the wiring so that all four pins go into the fan header) but you'd only be able to monitor the speed of one pump - same as the fans.
You might be best to add a PowerAdjust (standard only as the Aquaero will be in charge) and link it to the Aquaero with an Aquabus cable. Then you get a second flow sensor header and a fan header. That gives you enough for a header for each of the pump's and the 3 fan groups - although one of the would be volage control only.
Lots of info in the last few pages of the Aquaero thread on here too. Worth a read.
Hope that helps.