[nakano]

Honestly, over years of running shadowrun I have found a couple of tactics work best for me. 

1)  In any given game session, I normally have enough of a gameplan that I can anticipate the major matrix runs.  I try to get those done with the groups hacker/decker/technomancer during downtime/online.  This tends to work 75% of the time.  The hacker gets full sort of descriptives this way, but the information being sought, actions being taken are in the realm of "paydata" that remains undetermined until the session.  For intrusions I do the same thing, but pause the scene when the hacker is either in control of the critical node, or about to be fragged.

2)  For quick bits I will take the 5 minutes or so, but only if it is not going to screw up the flow of the game for the other players.  I have had deckers in groups in the past that have tried to do the private hack 3-4 times an hour, and have flatly said no.  I will give them a quick and dirty opposed dicepool roll, and count net successes and provide some info/options, but I will not allow one player to monopolize the game on a routine basis. 

That being said, I have run sessions that have been dominated by matrix ops, astral ops, info gathering, and surveillance.  It really comes down to what the party is interested in. 

[Dakka]

The visuals for the matrix run the gamut from the mundane to the extremely bizarre and how detailed you want or need to be regarding how actual programs look is group dependent.   The matrix as a whole however, the easiest way I've found to interpret it is the matrix itself is one giant node in which other nodes reside, since you can use a matrix perception test on a node before you attempt to enter it. 

Visually I've started imagining the sequence from Terminator Salvation where they are reprograming the infiltrator and he is accessing their mainframe, it shows what you could call nodes and visual links between them.  Alternately there is the Futurama version of the matrix (seen here) where the matrix is a giant cityscape where you could represent individual nodes as buildings, rooms, whatever.  The important thing to note is the ability to see a node from the outside before attempting a hack.

Having the Matrix team's combat run simultaneous with the ground teams combat is useful as a game pacing device, but I can't get over the coincidence of it all, the security team/gangers/random insect spirits/whatever happen to attack at the same time the hack goes horribly horribly wrong.  Instead you can have other players run agents to keep them involved or as nakano suggests get hacking completed before everyone is at the table.

[Darkeus]

I have always done simple rolls for Matrix activities unless it is a major part of the run.  The Matrix can be fiddly but I just try to keep it short and simple as to not drive myself crazy.