I like helping where I can, clarifying rules and taking part in interpretation questions is one of the ways that I work to improve the Shadowrun community.
As far as Wired Reflexes goes, my ruling has always been No. Ditto for the others. Basically, all those things affect the character's Physical Initiative, which is handled separately from the Matrix Initiative.
If you want to increase your Matrix Initiative Dice, there is a modification in Data Trails called the Multidimensional Coprocessor which gives you one more die, that plus going Hot-Sim will bump you up to the maximum 5 dice.
The owner of a slaved device in that case would be the Host. It would get alerted to potential intrusion and go on alert. Depending on the host, the response could be different. Generally, when I'm contemplating the Host's response I take into consideration things like the availability of a Security Spider, what sort of IC it runs, and of course what sort of host it is.
The Host at a local Stuffer Shack, for example, might queue up a bunch of IC to try and ward off against intrusion, but if it doesn't find anyone (if you haven't entered the host) it might calm back down after a few minutes. It would also probably alert the physical staff on-site to look for potential hackers, if you're hacking a security camera it means that you're either in the host already or you're direct connected.
The Host of a company might set the building security on alert as well, although it might wait for a security spider to make that call. Many Hosts probably see many attempts to hack them over the course of time, most are probably simple hit-and-runs that don't get past the initial attempts to get Marks.