Rather than argue whether or not the justice system has impacted blacks specifically, let's phrase it in terms of economic class. True, minorities in general have, statistically, lower average incomes than whites. Poor whites, Latinos, African-Americans and Native Americans all have much higher conviction rates in courts of law, as well as a much higher rate of using public defenders. With a disproportionate number of African-Americans in prison (the majority are still white, remember), it has had a predictable impact socially on the family unit, and life in the inner cities.
We would have to go back in time to understand how and under what circumstances laws have been made or changed in order to safeguard the rights of African American citizens. We could say that closer attention has been paid to the potentiality of bias during hearings, and more interest has grown as far as how law enforcement agents treat people of color versus white individuals.
This being said, we could argue that we are slowly learning how easy it is to take things for granted in society. Many forget that a number of cruel injustices have occurred to people of color throughout the years. However, since now we are speaking up and not taking it any longer, the criminal justice system is taking a closer look at due processes and ensuring with more strength what is due to all citizens regardless of color or creed.
In sociological terms this is a very interesting question because of the hugely disproportionate number of African Americans who are in custody. This fact alone begs serious questions to be asked about how representative, fair and just the American justice system is, as well as demanding an investigation into society at large to explore why this shocking statistic exists. It does not reflect well on the American justice system, to put it bluntly.
The criminal justice system has adversely affected the "black community." Look at the prison system and the percentages of incarcerated blacks vs incarcerated caucasians. Socio/economic standards play into this as well. Justice can be bought, so those who can afford better lawyers will more than likely have a better shot at staying out of jail or prison. One could also assert that the criminal justice system is therefore taking heads of families away from the black community, and thus perpetuating the problem.
This question is more suited to a book-length answer or more. To generalize as broadly as possible, I would point to two major impacts that the criminal justice system has had on the black community.
First, the criminal justice system has, especially recently, jailed much of the black male population. As the "crime" link below tells us,
Approximately 30 percent of African American males aged twenty to twenty-nine are under the control or supervision of the criminal justice system—four times as many as Caucasian men in the same age group.
This ends up having huge impacts on the community as these men lose much of their ability to ever find a good job after they get out. This contributes to lower marriage rates as women decline to marry men with low prospects. It also, of course, tends to increase poverty and crime.
Second, the sheer amount of negative contact with the police leads many in the black community to distrust the police completely. This negative contact ranges from the relatively trivial (people pulled over for "driving while black") to the very serious (black people shot by the police for what turned out to be no good reason). This has led to a great deal of hatred of the police.
There are many other ways in which the criminal justice system has impacted the black community, but these are the most important.